duplex: mafft/core/addsingle.c annotate

annotate mafft/core/addsingle.c @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

author	nick
date	Thu, 02 Feb 2017 18:44:31 -0500
parents
children

rev	line source
18 e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1 #include "mltaln.h"
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3 #define SMALLMEMORY 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	4
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	5 #define DEBUG 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	6 #define IODEBUG 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	7 #define SCOREOUT 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	8
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	9 static int nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	10 static int treein;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	11 static int topin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	12 static int treeout;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	13 static int distout;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	14 static int noalign;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	15 static int multidist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	16 static int maxdist = 2; // scale -> 2bai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	17 static int allowlongadds;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	18
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	19 static float lenfaca, lenfacb, lenfacc, lenfacd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	20 static int tuplesize;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	21
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	22 #define PLENFACA 0.01
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	23 #define PLENFACB 10000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	24 #define PLENFACC 10000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	25 #define PLENFACD 0.1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	26 #define D6LENFACA 0.01
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	27 #define D6LENFACB 2500
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	28 #define D6LENFACC 2500
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	29 #define D6LENFACD 0.1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	30 #define D10LENFACA 0.01
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	31 #define D10LENFACB 1000000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	32 #define D10LENFACC 1000000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	33 #define D10LENFACD 0.0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	34
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	35 typedef struct _thread_arg
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	36 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	37 int njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	38 int nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	39 int *nlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	40 int *follows;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	41 char **name;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	42 char **seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	43 LocalHom **localhomtable;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	44 float **iscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	45 float **nscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	46 int *istherenewgap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	47 int **newgaplist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	48 RNApair ***singlerna;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	49 double *eff_kozo_mapped;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	50 int alloclen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	51 Treedep *dep;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	52 int ***topol;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	53 float **len;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	54 Addtree *addtree;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	55 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	56 int *iaddshare;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	57 int thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	58 pthread_mutex_t *mutex_counter;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	59 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	60 } thread_arg_t;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	61
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	62
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	63 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	64 typedef struct _gaplist2alnxthread_arg
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	65 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	66 // int thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	67 int ncycle;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	68 int *jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	69 int tmpseqlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	70 int lenfull;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	71 char **seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	72 int *newgaplist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	73 int *posmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	74 pthread_mutex_t *mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	75 } gaplist2alnxthread_arg_t;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	76
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	77 typedef struct _distancematrixthread_arg
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	78 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	79 int thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	80 int njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	81 int norg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	82 int *jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	83 int **pointt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	84 int *nogaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	85 float **imtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	86 float **nmtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	87 float *selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	88 pthread_mutex_t *mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	89 } distancematrixthread_arg_t;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	90
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	91 typedef struct _jobtable2d
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	92 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	93 int i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	94 int j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	95 } Jobtable2d;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	96
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	97 typedef struct _dndprethread_arg
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	98 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	99 int njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	100 int thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	101 float *selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	102 float **mtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	103 char **seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	104 Jobtable2d *jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	105 pthread_mutex_t *mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	106 } dndprethread_arg_t;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	107
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	108 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	109
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	110 typedef struct _blocktorealign
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	111 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	112 int start;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	113 int end;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	114 int nnewres;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	115 } Blocktorealign;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	116
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	117 static void cnctintvec( int res, int o1, int *o2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	118 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	119 while( o1 != -1 ) res++ = *o1++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	120 while( o2 != -1 ) res++ = *o2++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	121 *res = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	122 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	123
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	124 static void countnewres( int len, Blocktorealign realign, int posmap, int *gaplist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	125 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	126 int i, regstart, regend, len1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	127 regstart = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	128 len1 = len+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	129 for( i=0; i<len1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	130 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	131 if( realign[i].nnewres \|\| gaplist[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	132 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	133 regend = posmap[i]-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	134 realign[i].start = regstart;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	135 realign[i].end = regend;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	136 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	137 if( gaplist[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	138 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	139 realign[i].nnewres++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	140 // fprintf( stderr, "hit? reg = %d-%d\n", regstart, regend );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	141 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	142 regstart = posmap[i]+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	143 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	144 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	145 static void fillgap( char *s, int len )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	146 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	147 int orilen = strlen( s );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	148 s += orilen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	149 len -= orilen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	150 while( len-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	151 *s++ = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	152 *s = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	153 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	154
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	155 static int lencomp( const void a, const void b ) // osoikamo
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	156 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	157 char ast = (char )a;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	158 char bst = (char )b;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	159 int lena = strlen( *ast );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	160 int lenb = strlen( *bst );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	161 // fprintf( stderr, "a=%s, b=%s\n", ast, bst );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	162 // fprintf( stderr, "lena=%d, lenb=%d\n", lena, lenb );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	163 if( lena > lenb ) return -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	164 else if( lena < lenb ) return 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	165 else return( 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	166 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	167
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	168 static int dorealignment_tree( Blocktorealign block, char fullseq, int fullseqlenpt, int norg, int **topol, int follows )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	169 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	170 int i, j, k, posinold, newlen, *nmem;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	171 int n0, n1, localloclen, nhit, hit1, hit2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	172 int *pickhistory;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	173 int nprof1, nprof2, pos, zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	174 char prof1, prof2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	175 int iinf0, iinf1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	176 int group, nearest, *g2n, ngroup;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	177 char ***mem;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	178 static char **tmpaln0 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	179 static char **tmpaln1 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	180 static char **tmpseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	181 int ***topolpick;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	182 int *tmpint;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	183 int intptr, intptrx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	184 char tmpseq0, cptr, **cptrptr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	185
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	186
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	187 localloclen = 4 * ( block->end - block->start + 1 ); // ookisugi?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	188 tmpaln0 = AllocateCharMtx( njob, localloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	189 tmpaln1 = AllocateCharMtx( njob, localloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	190 tmpseq = AllocateCharMtx( 1, fullseqlenpt 4 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	191 iinf0 = AllocateIntVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	192 iinf1 = AllocateIntVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	193 nearest = AllocateIntVec( njob ); // oosugi
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	194
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	195 posinold = block->start;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	196
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	197 n0 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	198 n1 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	199 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	200 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	201 strncpy( tmpseq[0], fullseq[i] + block->start, block->end - block->start + 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	202 tmpseq[0][block->end - block->start + 1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	203 commongappick( 1, tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	204 if( tmpseq[0][0] != 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	205 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	206 if( i < norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	207 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	208 fprintf( stderr, "BUG!!!!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	209 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	210 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	211 strcpy( tmpaln0[n0], tmpseq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	212 iinf0[n0] = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	213 nearest[n0] = follows[i-norg];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	214 n0++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	215 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	216 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	217 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	218 strcpy( tmpaln1[n0], "" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	219 iinf1[n1] = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	220 n1++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	221 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	222 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	223 mem = AllocateCharCub( n0, n0+1, 0 ); // oosugi
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	224 nmem = AllocateIntVec( n0 ); // oosugi
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	225 g2n = AllocateIntVec( n0 ); // oosugi
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	226 group = AllocateIntVec( n0 ); // oosugi
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	227 for( i=0; i<n0; i++ ) mem[i][0] = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	228 for( i=0; i<n0; i++ ) nmem[i] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	229 ngroup = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	230 for( i=0; i<n0; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	231 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	232 for( j=0; j<i; j++ ) if( nearest[j] == nearest[i] ) break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	233 if( j == i ) group[i] = ngroup++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	234 else group[i] = group[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	235
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	236 for( j=0; mem[group[i]][j]; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	237 ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	238 mem[group[i]][j] = tmpaln0[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	239 mem[group[i]][j+1] = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	240 nmem[group[i]]++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	241 g2n[group[i]] = nearest[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	242 // fprintf( stderr, "%d -> %d -> group%d\n", i, nearest[i], group[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	243 // fprintf( stderr, "mem[%d][%d] = %s\n", group[i], j, mem[group[i]][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	244 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	245
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	246 for( i=0; i<ngroup; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	247 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	248 // fprintf( stderr, "before sort:\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	249 // for( j=0; j<nmem[i]; j++ ) fprintf( stderr, "%s\n", mem[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	250 // fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	251 qsort( mem[i], nmem[i], sizeof( char * ), lencomp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	252 // fprintf( stderr, "after sort:\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	253 // for( j=0; j<nmem[i]; j++ ) fprintf( stderr, "%s\n", mem[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	254 // fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	255 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	256
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	257 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	258 for( i=1; i<n0; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	259 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	260 profilealignment( 1, n1, i, tmpaln0+i, tmpaln1, tmpaln0, localloclen, alg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	261 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	262 newlen = strlen( tmpaln0[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	263 for( i=0; i<n1; i++ ) eq2dash( tmpaln1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	264 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	265 // newlen = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	266 for( i=0; i<ngroup; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	267 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	268 // for( k=0; mem[i][k]; k++ ) fprintf( stderr, "mem[%d][%d] = %s\n", i, j, mem[i][k] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	269
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	270 for( j=1; j<nmem[i]; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	271 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	272 profilealignment2( 1, j, mem[i]+j, mem[i], localloclen, alg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	273 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	274 // for( j=0; j<nmem[i]; j++ ) fprintf( stderr, "j=%d, %s\n", j, mem[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	275
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	276 #if 0 // iru
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	277 if( ( j = strlen( mem[i][0] ) ) > newlen ) newlen = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	278 for( j=0; j<=i; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	279 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	280 for( k=0; mem[j][k]; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	281 fillgap( mem[j][k], newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	282 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	283 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	284
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	285 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	286 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	287 fprintf( stderr, "After ingroupalignment (original order):\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	288 for( i=0; i<n0; i++ ) fprintf( stderr, "%s\n", tmpaln0[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	289 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	290 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	291
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	292 topolpick = AllocateIntCub( ngroup, 2, ngroup );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	293 pickhistory = AllocateIntVec( ngroup );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	294 tmpint = AllocateIntVec( 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	295 prof1 = AllocateCharMtx( n0, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	296 prof2 = AllocateCharMtx( n0, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	297 for( i=0; i<ngroup; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	298 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	299 topolpick[i][0][0] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	300 topolpick[i][1][0] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	301 pickhistory[i] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	302 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	303
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	304 nhit = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	305 for( i=0; i<norg-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	306 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	307 for( intptr=topol[i][0]; *intptr>-1; intptr++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	308 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	309 for( intptrx=g2n,k=0; k<ngroup; intptrx++,k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	310 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	311 if( intptr == intptrx )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	312 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	313 hit1 = k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	314 goto exitloop1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	315 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	316 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	317 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	318 continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	319 exitloop1:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	320 // fprintf( stderr, "hit1! group%d -> %d\n", k, topol[i][0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	321
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	322 for( intptr=topol[i][1]; *intptr>-1; intptr++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	323 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	324 for( intptrx=g2n,k=0; k<ngroup; intptrx++,k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	325 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	326 if( intptr == intptrx )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	327 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	328 hit2 = k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	329 goto exitloop2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	330 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	331 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	332 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	333 continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	334 exitloop2:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	335
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	336 if( pickhistory[hit1] == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	337 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	338 topolpick[nhit][0][0] = hit1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	339 topolpick[nhit][0][1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	340 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	341 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	342 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	343 intcpy( topolpick[nhit][0], topolpick[pickhistory[hit1]][0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	344 intcat( topolpick[nhit][0], topolpick[pickhistory[hit1]][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	345 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	346 if( pickhistory[hit2] == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	347 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	348 topolpick[nhit][1][0] = hit2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	349 topolpick[nhit][1][1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	350 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	351 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	352 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	353 intcpy( topolpick[nhit][1], topolpick[pickhistory[hit2]][0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	354 intcat( topolpick[nhit][1], topolpick[pickhistory[hit2]][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	355 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	356
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	357 pickhistory[hit1] = nhit;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	358 pickhistory[hit2] = nhit;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	359 nhit++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	360 // g2n[hit1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	361 // g2n[hit2] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	362
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	363 // fprintf( stderr, "hit2! group%d -> %d\n", k, topol[i][1][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	364
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	365 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	366 fprintf( stderr, "\nHIT!!! \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	367 fprintf( stderr, "\nSTEP %d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	368 for( j=0; topol[i][0][j]>-1; j++ ) fprintf( stderr, "%3d ", topol[i][0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	369 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	370 for( j=0; topol[i][1][j]>-1; j++ ) fprintf( stderr, "%3d ", topol[i][1][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	371 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	372 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	373 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	374
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	375 for( i=0; i<ngroup-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	376 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	377 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	378 fprintf( stderr, "\npickSTEP %d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	379 for( j=0; topolpick[i][0][j]>-1; j++ ) fprintf( stderr, "%3d ", topolpick[i][0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	380 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	381 for( j=0; topolpick[i][1][j]>-1; j++ ) fprintf( stderr, "%3d ", topolpick[i][1][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	382 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	383 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	384
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	385 pos = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	386 // for( j=0; topolpick[i][0][j]>-1; j++ ) for( k=0; (cptr=mem[topolpick[i][0][j]][k]); k++ ) prof1[pos++] = cptr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	387 for( intptr=topolpick[i][0]; *intptr>-1; intptr++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	388 for( cptrptr=mem[intptr]; (cptr=cptrptr); cptrptr++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	389 prof1[pos++] = cptr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	390 nprof1 = pos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	391 pos = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	392 // for( j=0; topolpick[i][1][j]>-1; j++ ) for( k=0; (cptr=mem[topolpick[i][1][j]][k]); k++ ) prof2[pos++] = cptr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	393 for( intptr=topolpick[i][1]; *intptr>-1; intptr++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	394 for( cptrptr=mem[intptr]; (cptr=cptrptr); cptrptr++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	395 prof2[pos++] = cptr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	396 nprof2 = pos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	397
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	398
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	399 profilealignment2( nprof1, nprof2, prof1, prof2, localloclen, alg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	400 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	401 for( j=0; j<nprof1; j++ ) fprintf( stderr, "prof1[%d] = %s\n", j, prof1[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	402 for( j=0; j<nprof2; j++ ) fprintf( stderr, "prof2[%d] = %s\n", j, prof2[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	403 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	404 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	405 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	406 newlen = strlen( tmpaln0[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	407 for( j=0; j<n1; j++ ) fillgap( tmpaln1[j], newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	408
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	409 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	410 fprintf( stderr, "After rerealignment (original order):\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	411 for( i=0; i<n0; i++ ) fprintf( stderr, "%s\n", tmpaln0[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	412 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	413
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	414 // newlen = strlen( tmpaln0[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	415 zure = ( block->end - block->start + 1 - newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	416 // fprintf( stderr, "zure = %d, localloclen=%d, newlen=%d\n", zure, localloclen, newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	417
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	418
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	419 if( *fullseqlenpt < strlen( fullseq[0] ) - (block->end-block->start+1) + newlen + 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	420 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	421 fullseqlenpt = strlen( fullseq[0] ) 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	422 fprintf( stderr, "reallocating..." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	423 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	424 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	425 fullseq[i] = realloc( fullseq[i], fullseqlenpt sizeof( char ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	426 if( !fullseq[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	427 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	428 fprintf( stderr, "Cannot reallocate seq[][]\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	429 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	430 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	431 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	432 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	433 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	434
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	435
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	436 tmpseq0 = tmpseq[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	437 posinold = block->end+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	438 for( i=0; i<n0; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	439 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	440 strncpy( tmpseq0, tmpaln0[i], newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	441 strcpy( tmpseq0+newlen, fullseq[iinf0[i]] + posinold );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	442 strcpy( fullseq[iinf0[i]]+block->start, tmpseq0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	443 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	444 for( i=0; i<n1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	445 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	446 // eq2dash( tmpaln1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	447 strncpy( tmpseq0, tmpaln1[i], newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	448 strcpy( tmpseq0+newlen, fullseq[iinf1[i]] + posinold );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	449 strcpy( fullseq[iinf1[i]]+block->start, tmpseq0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	450 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	451 FreeCharMtx( tmpaln0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	452 FreeCharMtx( tmpaln1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	453 FreeCharMtx( tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	454 for( i=0; i<n0; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	455 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	456 // for( j=0; j<njob; j++ ) free( mem[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	457 free( mem[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	458 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	459 free( mem );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	460 free( nmem );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	461 free( iinf0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	462 free( iinf1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	463 free( group );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	464 free( g2n );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	465 free( prof1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	466 free( prof2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	467 free( nearest );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	468 FreeIntCub( topolpick );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	469 free( pickhistory );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	470 free( tmpint );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	471
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	472 return( zure );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	473 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	474
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	475
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	476 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	477 static int dorealignment( Blocktorealign block, char *fullseq, int alloclen, int fullseqlen, int norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	478 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	479 int i, posinnew, posinold, newlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	480 int n0, n1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	481 int zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	482 static int iinf0, iinf1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	483 static char **tmpaln0 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	484 static char **tmpaln1 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	485 static char **tmpseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	486 char opt, npt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	487
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	488 if( tmpaln0 == NULL )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	489 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	490 tmpaln0 = AllocateCharMtx( njob, alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	491 tmpaln1 = AllocateCharMtx( njob, alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	492 tmpseq = AllocateCharMtx( 1, fullseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	493 iinf0 = AllocateIntVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	494 iinf1 = AllocateIntVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	495 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	496 posinold = block->start;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	497
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	498
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	499 n0 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	500 n1 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	501 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	502 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	503 strncpy( tmpseq[0], fullseq[i] + block->start, block->end - block->start + 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	504 tmpseq[0][block->end - block->start + 1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	505 commongappick( 1, tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	506 // if( strlen( tmpseq[0] ) > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	507 if( tmpseq[0][0] != 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	508 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	509 if( i < norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	510 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	511 fprintf( stderr, "BUG!!!!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	512 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	513 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	514 strcpy( tmpaln0[n0], tmpseq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	515 iinf0[n0] = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	516 n0++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	517 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	518 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	519 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	520 strcpy( tmpaln1[n0], "" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	521 iinf1[n1] = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	522 n1++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	523 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	524 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	525
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	526
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	527 for( i=1; i<n0; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	528 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	529 profilealignment( 1, n1, i, tmpaln0+i, tmpaln1, tmpaln0, alloclen, alg ); // n1 ha allgap
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	530 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	531
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	532 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	533 fprintf( stderr, "After realignment:\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	534 for( i=0; i<n0; i++ ) fprintf( stderr, "%s\n", tmpaln0[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	535 // for( i=0; i<n1; i++ ) fprintf( stderr, "%s\n", tmpaln1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	536 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	537
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	538 newlen = strlen( tmpaln0[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	539 for( i=0; i<n0; i++ ) strncpy( fullseq[iinf0[i]]+block->start, tmpaln0[i], newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	540 for( i=0; i<n1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	541 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	542 eq2dash( tmpaln1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	543 strncpy( fullseq[iinf1[i]] + block->start, tmpaln1[i], newlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	544 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	545
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	546 posinold = block->end+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	547 posinnew = block->start + newlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	548
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	549
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	550 zure = ( block->end - block->start + 1 - strlen( tmpaln0[0] ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	551
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	552 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	553 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	554 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	555 strcpy( fullseq[i]+posinnew, fullseq[i]+posinold ); // ??
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	556 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	557 opt = fullseq[i] + posinold;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	558 npt = fullseq[i] + posinnew;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	559 while( ( npt++ = opt++ ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	560 *npt = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	561 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	562 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	563
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	564 return( zure );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	565 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	566 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	567
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	568 static void adjustposmap( int len, int posmap, int gaplist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	569 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	570 int *newposmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	571 int mpt1, mpt2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	572 int lenbk, zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	573 newposmap = calloc( len+2, sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	574 lenbk = len;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	575 zure = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	576 mpt1 = newposmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	577 mpt2 = posmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	578
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	579 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	580 int i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	581 fprintf( stderr, "posmapa = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	582 for( i=0; i<len+2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	583 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	584 fprintf( stderr, "%3d ", posmap[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	585 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	586 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	587 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	588
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	589 while( len-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	590 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	591 zure += *gaplist++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	592 mpt1++ = mpt2++ + zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	593 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	594 zure += *gaplist++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	595 mpt1 = mpt2 + zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	596
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	597 mpt1 = newposmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	598 mpt2 = posmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	599 len = lenbk;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	600 while( len-- ) mpt2++ = mpt1++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	601 mpt2 = mpt1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	602 free( newposmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	603 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	604 fprintf( stderr, "posmapm = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	605 for( i=0; i<lenbk+2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	606 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	607 fprintf( stderr, "%3d ", posmap[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	608 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	609 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	610 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	611 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	612
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	613 static int insertgapsbyotherfragments_compact( int len, char a, char s, int l, int p )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	614 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	615 int gaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	616 int i, pos, pi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	617 int prevp = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	618 int realignment = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	619 // fprintf( stderr, "### insertgapsbyotherfragments\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	620 for( i=0; i<len; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	621 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	622 gaplen = l[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	623 pi = p[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	624 pos = prevp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	625 // fprintf( stderr, "gaplen = %d\n", gaplen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	626 while( gaplen-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	627 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	628 pos++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	629 a++ = s++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	630 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	631 // fprintf( stderr, "pos = %d, pi = %d\n", pos, pi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	632 while( pos++ < pi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	633 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	634 *a++ = '=';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	635 realignment = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	636 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	637 a++ = s++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	638 prevp = pi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	639 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	640 gaplen = l[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	641 pi = p[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	642 pos = prevp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	643 while( gaplen-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	644 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	645 pos++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	646 a++ = s++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	647 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	648 while( pos++ < pi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	649 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	650 *a++ = '=';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	651 realignment = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	652 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	653 *a = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	654 return( realignment );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	655 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	656
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	657 void makegaplistcompact( int len, int p, int c, int *l )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	658 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	659 int i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	660 int pg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	661 int prep = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	662 for( i=0; i<len+2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	663 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	664 if( ( pg = p[i]-prep-1) > 0 && l[i] > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	665 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	666 if( pg < l[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	667 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	668 c[i] = l[i] - pg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	669 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	670 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	671 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	672 c[i] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	673 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	674 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	675 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	676 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	677 c[i] = l[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	678 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	679 prep = p[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	680 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	681 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	682
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	683
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	684 void gaplist2alnx( int len, char a, char s, int l, int p, int lenlimit )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	685 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	686 int gaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	687 int pos, pi, posl;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	688 int prevp = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	689 int reslen = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	690 char *sp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	691 // char *abk = a;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	692
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	693 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	694 int i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	695 char *abk = a;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	696 fprintf( stderr, "s = %s\n", s );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	697 fprintf( stderr, "posmap = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	698 for( i=0; i<len+2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	699 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	700 fprintf( stderr, "%3d ", p[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	701 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	702 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	703 fprintf( stderr, "gaplist = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	704 for( i=0; i<len+2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	705 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	706 fprintf( stderr, "%3d ", l[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	707 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	708 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	709 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	710 while( len-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	711 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	712 gaplen = *l++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	713 pi = *p++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	714
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	715 if( (reslen+=gaplen) > lenlimit )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	716 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	717 fprintf( stderr, "Length over. Please recompile!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	718 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	719 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	720 while( gaplen-- ) *a++ = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	721
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	722 pos = prevp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	723 sp = s + pos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	724 if( ( posl = pi - pos ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	725 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	726 if( ( reslen += posl ) > lenlimit )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	727 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	728 fprintf( stderr, "Length over. Please recompile\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	729 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	730 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	731 while( posl-- ) a++ = sp++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	732 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	733
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	734 if( reslen++ > lenlimit )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	735 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	736 fprintf( stderr, "Length over. Please recompile\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	737 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	738 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	739 a++ = sp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	740 prevp = pi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	741 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	742
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	743 gaplen = *l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	744 pi = *p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	745 if( (reslen+=gaplen) > lenlimit )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	746 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	747 fprintf( stderr, "Length over. Please recompile\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	748 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	749 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	750 while( gaplen-- ) *a++ = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	751
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	752 pos = prevp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	753 sp = s + pos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	754 if( ( posl = pi - pos ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	755 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	756 if( ( reslen += posl ) > lenlimit )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	757 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	758 fprintf( stderr, "Length over. Please recompile\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	759 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	760 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	761 while( posl-- ) a++ = sp++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	762 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	763 *a = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	764 // fprintf( stderr, "reslen = %d, strlen(a) = %d\n", reslen, strlen( abk ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	765 // fprintf( stderr, "a = %s\n", abk );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	766 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	767
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	768 static void makenewgaplist( int l, char a )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	769 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	770 while( 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	771 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	772 while( *a == '=' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	773 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	774 a++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	775 (*l)++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	776 // fprintf( stderr, "a[] (i) = %s, l=%d\n", a, (l) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	777 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	778 *++l = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	779 if( *a == 0 ) break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	780 a++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	781 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	782 *l = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	783 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	784
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	785
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	786 void arguments( int argc, char *argv[] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	787 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	788 int c;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	789
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	790 nthread = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	791 outnumber = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	792 scoreout = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	793 treein = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	794 topin = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	795 rnaprediction = 'm';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	796 rnakozo = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	797 nevermemsave = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	798 inputfile = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	799 addfile = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	800 addprofile = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	801 fftkeika = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	802 constraint = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	803 nblosum = 62;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	804 fmodel = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	805 calledByXced = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	806 devide = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	807 use_fft = 0; // chuui
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	808 force_fft = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	809 fftscore = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	810 fftRepeatStop = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	811 fftNoAnchStop = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	812 weight = 3;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	813 utree = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	814 tbutree = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	815 refine = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	816 check = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	817 cut = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	818 disp = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	819 outgap = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	820 alg = 'A';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	821 mix = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	822 tbitr = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	823 scmtd = 5;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	824 tbweight = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	825 tbrweight = 3;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	826 checkC = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	827 treemethod = 'X';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	828 sueff_global = 0.1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	829 contin = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	830 scoremtx = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	831 kobetsubunkatsu = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	832 dorp = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	833 ppenalty = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	834 penalty_shift_factor = 1000.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	835 ppenalty_ex = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	836 poffset = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	837 kimuraR = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	838 pamN = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	839 geta2 = GETA2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	840 fftWinSize = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	841 fftThreshold = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	842 RNAppenalty = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	843 RNAppenalty_ex = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	844 RNApthr = NOTSPECIFIED;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	845 TMorJTT = JTT;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	846 consweight_multi = 1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	847 consweight_rna = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	848 nadd = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	849 multidist = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	850 tuplesize = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	851 legacygapcost = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	852 allowlongadds = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	853
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	854 while( --argc > 0 && (*++argv)[0] == '-' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	855 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	856 while ( ( c = *++argv[0] ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	857 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	858 switch( c )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	859 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	860 case 'i':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	861 inputfile = *++argv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	862 fprintf( stderr, "inputfile = %s\n", inputfile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	863 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	864 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	865 case 'I':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	866 nadd = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	867 fprintf( stderr, "nadd = %d\n", nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	868 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	869 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	870 case 'e':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	871 RNApthr = (int)( atof( ++argv ) 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	872 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	873 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	874 case 'o':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	875 RNAppenalty = (int)( atof( ++argv ) 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	876 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	877 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	878 case 'f':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	879 ppenalty = (int)( atof( ++argv ) 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	880 // fprintf( stderr, "ppenalty = %d\n", ppenalty );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	881 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	882 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	883 case 'Q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	884 penalty_shift_factor = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	885 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	886 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	887 case 'g':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	888 ppenalty_ex = (int)( atof( ++argv ) 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	889 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	890 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	891 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	892 case 'h':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	893 poffset = (int)( atof( ++argv ) 1000 - 0.5 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	894 // fprintf( stderr, "poffset = %d\n", poffset );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	895 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	896 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	897 case 'k':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	898 kimuraR = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	899 fprintf( stderr, "kappa = %d\n", kimuraR );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	900 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	901 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	902 case 'b':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	903 nblosum = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	904 scoremtx = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	905 fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	906 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	907 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	908 case 'j':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	909 pamN = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	910 scoremtx = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	911 TMorJTT = JTT;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	912 fprintf( stderr, "jtt/kimura %d\n", pamN );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	913 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	914 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	915 case 'm':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	916 pamN = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	917 scoremtx = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	918 TMorJTT = TM;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	919 fprintf( stderr, "tm %d\n", pamN );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	920 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	921 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	922 case 'l':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	923 fastathreshold = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	924 constraint = 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	925 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	926 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	927 case 'r':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	928 consweight_rna = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	929 rnakozo = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	930 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	931 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	932 case 'c':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	933 consweight_multi = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	934 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	935 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	936 case 'C':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	937 nthread = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	938 fprintf( stderr, "nthread = %d\n", nthread );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	939 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	940 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	941 case 'R':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	942 rnaprediction = 'r';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	943 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	944 case 's':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	945 RNAscoremtx = 'r';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	946 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	947 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	948 case 'a':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	949 fmodel = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	950 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	951 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	952 case 'K':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	953 addprofile = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	954 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	955 case 'y':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	956 distout = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	957 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	958 case 't':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	959 treeout = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	960 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	961 case 'T':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	962 noalign = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	963 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	964 case 'D':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	965 dorp = 'd';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	966 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	967 case 'P':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	968 dorp = 'p';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	969 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	970 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	971 case 'O':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	972 outgap = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	973 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	974 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	975 case 'O':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	976 fftNoAnchStop = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	977 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	978 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	979 case 'S':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	980 scoreout = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	981 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	982 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	983 case 'e':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	984 fftscore = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	985 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	986 case 'r':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	987 fmodel = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	988 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	989 case 'R':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	990 fftRepeatStop = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	991 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	992 case 's':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	993 treemethod = 's';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	994 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	995 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	996 case 'X':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	997 treemethod = 'X';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	998 sueff_global = atof( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	999 fprintf( stderr, "sueff_global = %f\n", sueff_global );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1000 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1001 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1002 case 'E':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1003 treemethod = 'E';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1004 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1005 case 'q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1006 treemethod = 'q';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1007 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1008 case 'n' :
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1009 outnumber = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1010 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1011 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1012 case 'a':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1013 alg = 'a';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1014 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1015 case 'Q':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1016 alg = 'Q';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1017 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1018 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1019 case 'H':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1020 alg = 'H';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1021 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1022 case 'A':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1023 alg = 'A';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1024 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1025 case 'M':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1026 alg = 'M';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1027 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1028 case 'N':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1029 nevermemsave = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1030 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1031 case 'B':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1032 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1033 case 'F':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1034 use_fft = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1035 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1036 case 'G':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1037 force_fft = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1038 use_fft = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1039 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1040 case 'U':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1041 treein = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1042 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1043 case 'V':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1044 allowlongadds = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1045 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1046 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1047 case 'V':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1048 topin = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1049 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1050 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1051 case 'u':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1052 tbrweight = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1053 weight = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1054 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1055 case 'v':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1056 tbrweight = 3;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1057 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1058 case 'd':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1059 multidist = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1060 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1061 case 'W':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1062 tuplesize = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1063 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1064 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1065 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1066 case 'd':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1067 disp = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1068 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1069 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1070 /* Modified 01/08/27, default: user tree */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1071 case 'J':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1072 tbutree = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1073 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1074 /* modification end. */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1075 case 'z':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1076 fftThreshold = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1077 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1078 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1079 case 'w':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1080 fftWinSize = myatoi( *++argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1081 --argc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1082 goto nextoption;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1083 case 'Z':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1084 checkC = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1085 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1086 case 'L':
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1087 legacygapcost = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1088 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1089 default:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1090 fprintf( stderr, "illegal option %c\n", c );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1091 argc = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1092 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1093 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1094 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1095 nextoption:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1096 ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1097 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1098 if( argc == 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1099 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1100 cut = atof( (*argv) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1101 argc--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1102 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1103 if( argc != 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1104 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1105 fprintf( stderr, "options: Check source file !\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1106 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1107 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1108 if( tbitr == 1 && outgap == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1109 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1110 fprintf( stderr, "conflicting options : o, m or u\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1111 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1112 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1113 if( alg == 'C' && outgap == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1114 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1115 fprintf( stderr, "conflicting options : C, o\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1116 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1117 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1118 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1119
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1120
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1121 static float treebase( int nseq, int nlen, char aseq, int nadd, char mergeoralign, char mseq1, char mseq2, int **topol, double effarr, int alloclen, LocalHom localhomtable, RNApair *singlerna, double effarr_kozo )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1122 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1123 int i, l, m;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1124 int len1nocommongap, len2nocommongap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1125 int len1, len2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1126 int clus1, clus2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1127 float pscore, tscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1128 char indication1, indication2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1129 double *effarr1 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1130 double *effarr2 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1131 double *effarr1_kozo = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1132 double *effarr2_kozo = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1133 LocalHom ***localhomshrink = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1134 int *fftlog;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1135 int m1, m2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1136 int *gaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1137 int *gapmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1138 int *alreadyaligned;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1139 float dumfl = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1140 int ffttry;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1141 RNApair *grouprna1, *grouprna2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1142
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1143 if( rnakozo && rnaprediction == 'm' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1144 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1145 grouprna1 = (RNApair *)calloc( nseq, sizeof( RNApair ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1146 grouprna2 = (RNApair *)calloc( nseq, sizeof( RNApair ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1147 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1148 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1149 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1150 grouprna1 = grouprna2 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1151 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1152
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1153 fftlog = AllocateIntVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1154 effarr1 = AllocateDoubleVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1155 effarr2 = AllocateDoubleVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1156 indication1 = AllocateCharVec( 150 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1157 indication2 = AllocateCharVec( 150 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1158 alreadyaligned = AllocateIntVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1159 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1160 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1161 localhomshrink = (LocalHom *)calloc( nseq, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1162 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1163 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1164 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1165 for( i=0; i<nseq; i++) localhomshrink[i] = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1166 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1167 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1168 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1169 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1170 for( i=0; i<nseq; i++) localhomshrink[i] = (LocalHom *)calloc( nseq, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1171 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1172 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1173 effarr1_kozo = AllocateDoubleVec( nseq ); //tsuneni allocate sareru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1174 effarr2_kozo = AllocateDoubleVec( nseq ); //tsuneni allocate sareru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1175 for( i=0; i<nseq; i++ ) effarr1_kozo[i] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1176 for( i=0; i<nseq; i++ ) effarr2_kozo[i] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1177
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1178 gaplen = AllocateIntVec( *alloclen+10 ); // maikai shokika
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1179 gapmap = AllocateIntVec( *alloclen+10 ); // maikai shokika
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1180 for( i=0; i<nseq-1; i++ ) alreadyaligned[i] = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1181 alreadyaligned[nseq-1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1182
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1183 for( l=0; l<nseq; l++ ) fftlog[l] = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1184
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1185
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1186 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1187 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1188 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1189 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1190 dontcalcimportance_firstone( nseq, effarr, aseq, localhomtable );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1191 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1192 calcimportance( nseq, effarr, aseq, localhomtable );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1193 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1194 calcimportance( nseq, effarr, aseq, localhomtable );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1195 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1196 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1197
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1198 tscore = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1199 for( l=0; l<nseq-1; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1200 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1201 if( mergeoralign[l] == 'n' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1202 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1203 // fprintf( stderr, "SKIP!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1204 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1205 free( topol[l][0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1206 free( topol[l][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1207 free( topol[l] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1208 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1209 continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1210 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1211
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1212 m1 = topol[l][0][0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1213 m2 = topol[l][1][0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1214 len1 = strlen( aseq[m1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1215 len2 = strlen( aseq[m2] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1216 if( *alloclen < len1 + len2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1217 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1218 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1219 fprintf( stderr, "\nReallocating.." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1220 *alloclen = ( len1 + len2 ) + 1000;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1221 ReallocateCharMtx( aseq, nseq, *alloclen + 10 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1222 gaplen = realloc( gaplen, ( alloclen + 10 ) sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1223 if( gaplen == NULL )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1224 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1225 fprintf( stderr, "Cannot realloc gaplen\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1226 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1227 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1228 gapmap = realloc( gapmap, ( alloclen + 10 ) sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1229 if( gapmap == NULL )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1230 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1231 fprintf( stderr, "Cannot realloc gapmap\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1232 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1233 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1234 fprintf( stderr, "done. alloclen = %d\n", alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1235 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1236 fprintf( stderr, "Length over!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1237 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1238 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1239 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1240
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1241 if( effarr_kozo )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1242 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1243 clus1 = fastconjuction_noname_kozo( topol[l][0], aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1244 clus2 = fastconjuction_noname_kozo( topol[l][1], aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1245 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1246 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1247 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1248 clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1, 0.0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1249 clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2, 0.0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1250 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1251
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1252 if( mergeoralign[l] == '1' \|\| mergeoralign[l] == '2' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1253 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1254 newgapstr = "=";
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1255 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1256 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1257 newgapstr = "-";
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1258
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1259
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1260 len1nocommongap = len1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1261 len2nocommongap = len2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1262 if( mergeoralign[l] == '1' ) // nai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1263 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1264 findcommongaps( clus2, mseq2, gapmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1265 commongappick( clus2, mseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1266 len2nocommongap = strlen( mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1267 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1268 else if( mergeoralign[l] == '2' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1269 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1270 findcommongaps( clus1, mseq1, gapmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1271 commongappick( clus1, mseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1272 len1nocommongap = strlen( mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1273 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1274
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1275
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1276 // fprintf( trap_g, "\nSTEP-%d\n", l );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1277 // fprintf( trap_g, "group1 = %s\n", indication1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1278 // fprintf( trap_g, "group2 = %s\n", indication2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1279 //
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1280 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1281 // fprintf( stderr, "\rSTEP % 5d /%d ", l+1, nseq-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1282 // fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1283 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1284 fprintf( stdout, "STEP %d /%d\n", l+1, nseq-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1285 fprintf( stderr, "STEP %d /%d\n", l+1, nseq-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1286 fprintf( stderr, "group1 = %.66s", indication1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1287 if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1288 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1289 fprintf( stderr, "group2 = %.66s", indication2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1290 if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1291 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1292 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1293
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1294
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1295
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1296 // for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1297
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1298 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1299 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1300 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1301 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1302 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1303 fastshrinklocalhom_one( topol[l][0], topol[l][1], nseq-1, localhomtable, localhomshrink );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1304 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1305 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1306 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1307 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1308 fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1309 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1310
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1311 // msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1312 // fprintf( stdout, "localhomshrink =\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1313 // outlocalhompt( localhomshrink, clus1, clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1314 // weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1315 // fprintf( stderr, "after weight =\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1316 // outlocalhompt( localhomshrink, clus1, clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1317 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1318 if( rnakozo && rnaprediction == 'm' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1319 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1320 makegrouprna( grouprna1, singlerna, topol[l][0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1321 makegrouprna( grouprna2, singlerna, topol[l][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1322 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1323
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1324
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1325 /*
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1326 fprintf( stderr, "before align all\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1327 display( aseq, nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1328 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1329 fprintf( stderr, "before align 1 %s \n", indication1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1330 display( mseq1, clus1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1331 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1332 fprintf( stderr, "before align 2 %s \n", indication2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1333 display( mseq2, clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1334 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1335 */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1336
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1337
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1338 if( !nevermemsave && ( constraint != 2 && alg != 'M' && ( len1 > 30000 \|\| len2 > 30000 ) ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1339 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1340 fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1341 alg = 'M';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1342 if( commonIP ) FreeIntMtx( commonIP );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1343 commonIP = NULL; // 2013/Jul17
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1344 commonAlloc1 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1345 commonAlloc2 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1346 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1347
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1348
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1349 // if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1350 if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1351 else ffttry = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1352 // ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1353 // fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1354 // fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1355 if( constraint == 2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1356 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1357 if( alg == 'M' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1358 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1359 fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1360 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1361 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1362 fprintf( stderr, "c" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1363 if( alg == 'A' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1364 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1365 imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1366 if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1367 pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1368 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1369 else if( alg == 'Q' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1370 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1371 fprintf( stderr, "Q has been disabled.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1372 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1373 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1374 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1375 else if( force_fft \|\| ( use_fft && ffttry ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1376 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1377 fprintf( stderr, "f" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1378 if( alg == 'M' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1379 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1380 fprintf( stderr, "m" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1381 pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, *alloclen, fftlog+m1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1382 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1383 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1384 pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, *alloclen, fftlog+m1, NULL, 0, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1385 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1386 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1387 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1388 fprintf( stderr, "d" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1389 fftlog[m1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1390 switch( alg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1391 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1392 case( 'a' ):
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1393 pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1394 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1395 case( 'M' ):
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1396 fprintf( stderr, "m" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1397 pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1398 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1399 case( 'A' ):
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1400 pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1401 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1402 default:
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1403 ErrorExit( "ERROR IN SOURCE FILE" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1404 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1405 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1406
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1407
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1408 nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1409
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1410 // fprintf( stderr, "aseq[last] = %s\n", aseq[nseq-1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1411
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1412 #if SCOREOUT
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1413 fprintf( stderr, "score = %10.2f\n", pscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1414 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1415 tscore += pscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1416 #if 0 // New gaps = '='
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1417 fprintf( stderr, "Original msa\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1418 for( i=0; i<clus1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1419 fprintf( stderr, "%s\n", mseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1420 fprintf( stderr, "Query\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1421 for( i=0; i<clus2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1422 fprintf( stderr, "%s\n", mseq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1423 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1424
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1425 // writePre( nseq, name, nlen, aseq, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1426
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1427 if( disp ) display( aseq, nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1428
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1429 if( mergeoralign[l] == '1' ) // jissainiha nai. atarashii hairetsu ha saigo dakara.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1430 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1431 adjustgapmap( strlen( mseq2[0] )-len2nocommongap+len2, gapmap, mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1432 restorecommongaps( nseq, aseq, topol[l][0], topol[l][1], gapmap, *alloclen, '-' );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1433 findnewgaps( clus2, 0, mseq2, gaplen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1434 insertnewgaps( nseq, alreadyaligned, aseq, topol[l][1], topol[l][0], gaplen, gapmap, *alloclen, alg, '-' );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1435 // for( i=0; i<nseq; i++ ) eq2dash( aseq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1436 for( i=0; (m=topol[l][0][i])>-1; i++ ) alreadyaligned[m] = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1437 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1438 if( mergeoralign[l] == '2' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1439 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1440 adjustgapmap( strlen( mseq1[0] )-len1nocommongap+len1, gapmap, mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1441 restorecommongaps( nseq, aseq, topol[l][0], topol[l][1], gapmap, *alloclen, '-' );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1442 findnewgaps( clus1, 0, mseq1, gaplen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1443 insertnewgaps( nseq, alreadyaligned, aseq, topol[l][0], topol[l][1], gaplen, gapmap, *alloclen, alg, '-' );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1444 // for( i=0; i<nseq; i++ ) eq2dash( aseq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1445 for( i=0; (m=topol[l][1][i])>-1; i++ ) alreadyaligned[m] = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1446 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1447
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1448 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1449 free( topol[l][0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1450 free( topol[l][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1451 free( topol[l] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1452 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1453 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1454
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1455 #if SCOREOUT
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1456 fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1457 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1458 free( gaplen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1459 free( gapmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1460 if( rnakozo && rnaprediction == 'm' )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1461 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1462 free( grouprna1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1463 free( grouprna2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1464 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1465 free( fftlog ); // iranai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1466 free( effarr1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1467 free( effarr2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1468 free( indication1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1469 free( indication2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1470 free( alreadyaligned );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1471 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1472 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1473 for( i=0; i<nseq; i++ ) free( localhomshrink[i] ); // ??
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1474 free( localhomshrink );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1475 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1476 free( effarr1_kozo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1477 free( effarr2_kozo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1478
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1479 return( pscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1480 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1481
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1482
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1483
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1484
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1485 static void mtxcpy( int norg, int njobc, float *iscorec, float iscore )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1486 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1487 int i, nlim, n;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1488 float fpt, fptc;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1489
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1490 *iscorec = AllocateFloatHalfMtx( njobc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1491 nlim = norg-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1492 for( i=0; i<nlim; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1493 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1494 fptc = (*iscorec)[i]+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1495 fpt = iscore[i]+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1496 n = norg-i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1497 while( n-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1498 fptc++ = fpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1499 // for( j=i+1; j<norg; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1500 // (*iscorec)[i][j-i] = iscore[i][j-i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1501 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1502 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1503
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1504
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1505 static void addsinglethread( void arg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1506 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1507 thread_arg_t targ = (thread_arg_t )arg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1508 int *nlenc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1509 char **namec = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1510 Treedep *depc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1511 char mseq1 = NULL, mseq2 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1512 float **iscorec;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1513 // float **iscorecbk; // to speedup
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1514 double *effc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1515 int ***topolc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1516 float **lenc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1517 LocalHom **localhomtablec = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1518 int *memlist0 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1519 int *memlist1 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1520 int *addmem = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1521 int njobc, norg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1522 char **bseq = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1523 int i, j, k, m, iadd, rep, neighbor;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1524 char *mergeoralign = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1525 int *nogaplenjusttodecideaddhereornot = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1526 char *tmpseq = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1527
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1528 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1529 int thread_no = targ->thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1530 int *iaddshare = targ->iaddshare;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1531 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1532 int njob = targ->njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1533 int *follows = targ->follows;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1534 int nadd = targ->nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1535 int *nlen = targ->nlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1536 char **name = targ->name;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1537 char **seq = targ->seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1538 LocalHom **localhomtable = targ->localhomtable;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1539 float **iscore = targ->iscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1540 float **nscore = targ->nscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1541 int *istherenewgap = targ->istherenewgap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1542 int **newgaplist = targ->newgaplist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1543 RNApair ***singlerna = targ->singlerna;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1544 double *eff_kozo_mapped = targ->eff_kozo_mapped;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1545 int alloclen = targ->alloclen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1546 Treedep *dep = targ->dep;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1547 int ***topol = targ->topol;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1548 float **len = targ->len;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1549 Addtree *addtree = targ->addtree;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1550 float pscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1551 int *alnleninnode = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1552 char *targetseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1553
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1554
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1555 // fprintf( stderr, "\nPreparing thread %d\n", thread_no );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1556 norg = njob - nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1557 njobc = norg+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1558
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1559 alnleninnode = AllocateIntVec( norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1560 addmem = AllocateIntVec( nadd+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1561 depc = (Treedep *)calloc( njobc, sizeof( Treedep ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1562 mseq1 = AllocateCharMtx( njob, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1563 mseq2 = AllocateCharMtx( njob, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1564 bseq = AllocateCharMtx( njobc, alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1565 namec = AllocateCharMtx( njob, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1566 nlenc = AllocateIntVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1567 mergeoralign = AllocateCharVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1568 nogaplenjusttodecideaddhereornot = AllocateIntVec( njobc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1569 tmpseq = calloc( alloclen, sizeof( char ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1570
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1571 if( allowlongadds ) // hontou ha iranai.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1572 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1573 for( i=0; i<njobc; i++ ) nogaplenjusttodecideaddhereornot[i] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1574 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1575 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1576 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1577 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1578 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1579 gappick0( tmpseq, seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1580 nogaplenjusttodecideaddhereornot[i] = strlen( tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1581 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1582 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1583
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1584 for( i=0; i<norg; i++ ) strcpy( bseq[i], seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1585 if( norg == 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1586 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1587 alnleninnode[0] = strlen( bseq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1588 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1589 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1590 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1591 for( i=norg-2; i>=0; i-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1592 // for( i=norg-2; i; i-- ) // BUG!!!!
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1593 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1594 // reporterr( "\nstep %d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1595 k = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1596 for( j=0; (m=topol[i][0][j])!=-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1597 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1598 mseq1[k++] = bseq[m];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1599 // reporterr( "%d ", m );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1600 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1601 for( j=0; (m=topol[i][1][j])!=-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1602 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1603 mseq1[k++] = bseq[m];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1604 // reporterr( "%d ", m );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1605 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1606 // reporterr( "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1607 commongappick( k, mseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1608 alnleninnode[i] = strlen( mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1609 // fprintf( stderr, "alnleninnode[%d] = %d\n", i, alnleninnode[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1610 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1611 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1612 // for( i=0; i<norg-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1613 // fprintf( stderr, "alnleninnode[%d] = %d\n", i, alnleninnode[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1614
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1615
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1616 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1617 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1618 localhomtablec = (LocalHom *)calloc( njobc, sizeof( LocalHom ) ); // motto chiisaku dekiru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1619 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1620 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1621 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1622 for( i=0; i<njobc; i++) localhomtablec[i] = (LocalHom *)calloc( 1, sizeof( LocalHom ) ); // motto chiisaku dekiru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1623 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1624 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1625 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1626 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1627 for( i=0; i<njobc; i++) localhomtablec[i] = (LocalHom *)calloc( njobc, sizeof( LocalHom ) ); // motto chiisaku dekiru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1628 for( i=0; i<norg; i++ ) for( j=0; j<norg; j++ ) localhomtablec[i][j] = localhomtable[i][j]; // iru!
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1629 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1630 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1631
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1632
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1633 topolc = AllocateIntCub( njobc, 2, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1634 lenc = AllocateFloatMtx( njobc, 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1635 effc = AllocateDoubleVec( njobc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1636 // for( i=0; i<norg; i++ ) nlenc[i] = strlen( seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1637 for( i=0; i<norg; i++ ) nlenc[i] = nlen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1638 for( i=0; i<norg; i++ ) namec[i] = name[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1639 memlist0 = AllocateIntVec( norg+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1640 memlist1 = AllocateIntVec( 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1641 for( i=0; i<norg; i++ ) memlist0[i] = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1642 memlist0[norg] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1643
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1644 // fprintf( stderr, "\ndone. %d\n", thread_no );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1645
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1646 // mtxcpy( norg, norg, &iscorecbk, iscore ); // to speedup?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1647
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1648
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1649 iadd = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1650 while( 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1651 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1652 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1653 if( nthread )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1654 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1655 pthread_mutex_lock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1656 iadd = *iaddshare;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1657 if( iadd == nadd )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1658 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1659 pthread_mutex_unlock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1660 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1661 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1662 fprintf( stderr, "\r%d / %d (thread %d) \r", iadd, nadd, thread_no );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1663 ++(*iaddshare);
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1664 targetseq = seq[norg+iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1665 pthread_mutex_unlock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1666 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1667 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1668 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1669 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1670 iadd++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1671 targetseq = seq[norg+iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1672 if( iadd == nadd ) break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1673 fprintf( stderr, "\r%d / %d \r", iadd, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1674 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1675
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1676 for( i=0; i<norg; i++ ) strcpy( bseq[i], seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1677 // gappick0( bseq[norg], seq[norg+iadd] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1678 gappick0( bseq[norg], targetseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1679
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1680 if( allowlongadds ) // missed in v7.220
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1681 nogaplenjusttodecideaddhereornot[norg] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1682 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1683 nogaplenjusttodecideaddhereornot[norg] = strlen( bseq[norg] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1684
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1685 mtxcpy( norg, njobc, &iscorec, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1686
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1687 if( multidist \|\| tuplesize > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1688 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1689 for( i=0; i<norg; i++ ) iscorec[i][norg-i] = nscore[i][iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1690 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1691 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1692 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1693 for( i=0; i<norg; i++ ) iscorec[i][norg-i] = iscore[i][norg+iadd-i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1694 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1695
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1696
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1697 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1698 for( i=0; i<njobc-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1699 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1700 fprintf( stderr, "i=%d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1701 for( j=i+1; j<njobc; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1702 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1703 fprintf( stderr, "%d-%d, %f\n", i, j, iscorec[i][j-i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1704 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1705 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1706 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1707 nlenc[norg] = nlen[norg+iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1708 namec[norg] = name[norg+iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1709 if( constraint)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1710 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1711 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1712 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1713 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1714 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1715 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1716 localhomtablec[i][0] = localhomtable[i][iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1717 // localhomtablec[norg][i] = localhomtable[norg+iadd][i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1718 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1719 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1720 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1721 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1722 localhomtablec[i][norg] = localhomtable[i][norg+iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1723 localhomtablec[norg][i] = localhomtable[norg+iadd][i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1724 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1725 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1726 // localhomtablec[norg][norg] = localhomtable[norg+iadd][norg+iadd]; // iranai!!
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1727 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1728
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1729 // fprintf( stderr, "Constructing a UPGMA tree %d ... ", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1730 // fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1731
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1732
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1733 // if( iadd == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1734 // {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1735 // }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1736 // fixed_musclesupg_float_realloc_nobk_halfmtx( njobc, iscorec, topolc, lenc, depc, 0, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1737 neighbor = addonetip( njobc, topolc, lenc, iscorec, topol, len, dep, treeout, addtree, iadd, name, alnleninnode, nogaplenjusttodecideaddhereornot, noalign );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1738
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1739
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1740 FreeFloatHalfMtx( iscorec, njobc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1741
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1742
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1743 if( tbrweight )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1744 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1745 weight = 3;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1746 counteff_simple_float_nostatic( njobc, topolc, lenc, effc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1747 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1748 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1749 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1750 for( i=0; i<njobc; i++ ) effc[i] = 1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1751 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1752
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1753 // FreeFloatMtx( lenc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1754
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1755 if( noalign ) // nen no tame weight wo keisan.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1756 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1757 // FreeFloatHalfMtx( iscorec, njobc ); // saki ni continue suru baai ha fukkatsu.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1758 continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1759 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1760
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1761 // reporterr( "iadd = %d\n", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1762
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1763 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1764 for( i=0; i<njobc-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1765 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1766 fprintf( stderr, "\n step %d\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1767 fprintf( stderr, "topol[%d] = \n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1768 for( j=0; topolc[i][0][j]!=-1; j++ ) fprintf( stderr, "%d ", topolc[i][0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1769 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1770 fprintf( stderr, "len=%f\n", lenc [i][0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1771 for( j=0; topolc[i][1][j]!=-1; j++ ) fprintf( stderr, "%d ", topolc[i][1][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1772 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1773 fprintf( stderr, "len=%f\n", lenc [i][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1774 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1775
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1776 fprintf( stderr, "\nneighbor = %d, iadd = %d\n", neighbor, iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1777 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1778 follows[iadd] = neighbor;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1779
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1780 for( i=0; i<njobc-1; i++ ) mergeoralign[i] = 'n';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1781 for( j=njobc-1; j<njobc; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1782 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1783 addmem[0] = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1784 addmem[1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1785 for( i=0; i<njobc-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1786 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1787 if( samemembern( topolc[i][0], addmem, 1 ) ) // arieru
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1788 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1789 // fprintf( stderr, "HIT!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1790 if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1791 else mergeoralign[i] = '1';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1792 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1793 else if( samemembern( topolc[i][1], addmem, 1 ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1794 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1795 // fprintf( stderr, "HIT!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1796 if( mergeoralign[i] != 'n' ) mergeoralign[i] = 'w';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1797 else mergeoralign[i] = '2';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1798 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1799 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1800 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1801
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1802 // for( i=0; i<1; i++ ) addmem[i] = njobc-1+i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1803 addmem[0] = njobc-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1804 addmem[1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1805 for( i=0; i<njobc-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1806 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1807 if( includemember( topolc[i][0], addmem ) && includemember( topolc[i][1], addmem ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1808 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1809 mergeoralign[i] = 'w';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1810 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1811 else if( includemember( topolc[i][0], addmem ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1812 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1813 mergeoralign[i] = '1';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1814 // fprintf( stderr, "HIT 1! iadd=%d", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1815 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1816 else if( includemember( topolc[i][1], addmem ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1817 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1818 mergeoralign[i] = '2';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1819 // fprintf( stderr, "HIT 2! iadd=%d", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1820 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1821 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1822 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1823 for( i=0; i<njob-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1824 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1825 fprintf( stderr, "mem0 = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1826 for( j=0; topol[i][0][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][0][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1827 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1828 fprintf( stderr, "mem1 = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1829 for( j=0; topol[i][1][j]>-1; j++ ) fprintf( stderr, "%d ", topol[i][1][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1830 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1831 fprintf( stderr, "i=%d, mergeoralign[] = %c\n", i, mergeoralign[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1832 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1833 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1834
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1835
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1836 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1837 for( i=0; i<norg; i++ ) fprintf( stderr, "seq[%d, iadd=%d] = \n%s\n", i, iadd, seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1838 fprintf( stderr, "gapmapS (iadd=%d) = \n", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1839 for( i=0; i<lennocommongap; i++ ) fprintf( stderr, "%d\n", gapmapS[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1840 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1841
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1842
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1843 // fprintf( stderr, "Progressive alignment ... \r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1844
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1845 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1846 pthread_mutex_lock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1847 fprintf( stdout, "\nmergeoralign (iadd=%d) = ", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1848 for( i=0; i<njobc-1; i++ ) fprintf( stdout, "%c", mergeoralign[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1849 fprintf( stdout, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1850 pthread_mutex_unlock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1851 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1852 singlerna = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1853 pscore = treebase( njobc, nlenc, bseq, 1, mergeoralign, mseq1, mseq2, topolc, effc, &alloclen, localhomtablec, singlerna, eff_kozo_mapped );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1854 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1855 pthread_mutex_lock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1856 // fprintf( stdout, "res (iadd=%d) = %s, pscore=%f\n", iadd, bseq[norg], pscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1857 // fprintf( stdout, "effc (iadd=%d) = ", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1858 // for( i=0; i<njobc; i++ ) fprintf( stdout, "%f ", effc[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1859 // fprintf( stdout, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1860 pthread_mutex_unlock( targ->mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1861 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1862
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1863
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1864 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1865 fprintf( trap_g, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1866 fclose( trap_g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1867 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1868 // fprintf( stdout, "\n>seq[%d, iadd=%d] = \n%s\n", norg+iadd, iadd, seq[norg+iadd] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1869 // fprintf( stdout, "\n>bseq[%d, iadd=%d] = \n%s\n", norg, iadd, bseq[norg] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1870
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1871 // strcpy( seq[norg+iadd], bseq[norg] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1872 strcpy( targetseq, bseq[norg] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1873
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1874 rep = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1875 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1876 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1877 // fprintf( stderr, "Checking %d/%d\n", i, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1878 if( strchr( bseq[i], '=' ) ) break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1879 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1880 if( i == norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1881 istherenewgap[iadd] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1882 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1883 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1884 rep = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1885 istherenewgap[iadd] = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1886 makenewgaplist( newgaplist[iadd], bseq[rep] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1887 // for( i=0; newgaplist[iadd][i]!=-1; i++ ) fprintf( stderr, "%d: %d\n", i, newgaplist[iadd][i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1888 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1889 eq2dash( targetseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1890
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1891 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1892
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1893
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1894 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1895 if( constraint && localhomtablec )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1896 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1897 for( i=0; i<njobc; i++ ) free( localhomtablec[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1898 free( localhomtablec );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1899 localhomtablec = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1900 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1901 if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1902 if( nogaplenjusttodecideaddhereornot ) free( nogaplenjusttodecideaddhereornot ); nogaplenjusttodecideaddhereornot = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1903 if( alnleninnode ) free( alnleninnode ); alnleninnode = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1904 if( tmpseq ) free( tmpseq ); tmpseq = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1905 if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1906 if( namec ) free( namec ); namec = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1907 if( nlenc ) free( nlenc ); nlenc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1908 if( depc ) free( depc ); depc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1909 if( topolc ) FreeIntCub( topolc ); topolc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1910 if( lenc ) FreeFloatMtx( lenc ); lenc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1911 if( effc ) FreeDoubleVec( effc ); effc = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1912 if( memlist0 ) free( memlist0 ); memlist0 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1913 if( memlist1 ) free( memlist1 ); memlist1 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1914 if( addmem ) free( addmem ); addmem = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1915 if( mseq1 ) free( mseq1 ); mseq1 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1916 if( mseq2 ) free( mseq2 ); mseq2 = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1917 Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1918 A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1919 if( commonIP ) FreeIntMtx( commonIP );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1920 commonIP = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1921 commonAlloc1 = commonAlloc2 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1922 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1923 // FreeFloatHalfMtx( iscorecbk, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1924
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1925 return( NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1926 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1927
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1928 static int maxl;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1929 static int tsize;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1930 static int nunknown = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1931
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1932 void seq_grp_nuc( int grp, char seq )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1933 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1934 int tmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1935 int *grpbk = grp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1936 while( *seq )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1937 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1938 tmp = amino_grp[(int)*seq++];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1939 if( tmp < 4 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1940 *grp++ = tmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1941 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1942 nunknown++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1943 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1944 *grp = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1945 if( grp - grpbk < tuplesize )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1946 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1947 // fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1948 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1949 *grpbk = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1950 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1951 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1952
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1953 void seq_grp( int grp, char seq )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1954 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1955 int tmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1956 int *grpbk = grp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1957 while( *seq )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1958 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1959 tmp = amino_grp[(int)*seq++];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1960 if( tmp < 6 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1961 *grp++ = tmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1962 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1963 nunknown++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1964 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1965 *grp = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1966 if( grp - grpbk < 6 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1967 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1968 // fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1969 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1970 *grpbk = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1971 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1972 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1973
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1974 void makecompositiontable_p( int table, int pointt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1975 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1976 int point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1977
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1978 while( ( point = *pointt++ ) != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1979 table[point]++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1980 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1981
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1982 int commonsextet_p( int table, int pointt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1983 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1984 int value = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1985 int tmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1986 int point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1987 static TLS int *memo = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1988 static TLS int *ct = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1989 int *cp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1990
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1991 if( table == NULL )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1992 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1993 if( memo ) free( memo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1994 if( ct ) free( ct );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1995 return( 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1996 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1997
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1998 if( *pointt == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1999 return( 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2001 if( !memo )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2002 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2003 memo = (int *)calloc( tsize, sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2004 if( !memo ) ErrorExit( "Cannot allocate memo\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2005 ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) ); // chuui!!
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2006 if( !ct ) ErrorExit( "Cannot allocate ct\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2007 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2008
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2009 cp = ct;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2010 while( ( point = *pointt++ ) != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2011 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2012 tmp = memo[point]++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2013 if( tmp < table[point] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2014 value++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2015 if( tmp == 0 ) *cp++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2016 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2017 *cp = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2018
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2019 cp = ct;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2020 while( *cp != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2021 memo[*cp++] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2022
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2023 return( value );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2024 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2025
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2026 void makepointtable_nuc_dectet( int pointt, int n )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2027 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2028 int point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2029 register int *p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2030
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2031 if( *n == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2032 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2033 *pointt = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2034 return;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2035 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2036
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2037 p = n;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2038 point = n++ 262144;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2039 point += n++ 65536;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2040 point += n++ 16384;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2041 point += n++ 4096;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2042 point += n++ 1024;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2043 point += n++ 256;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2044 point += n++ 64;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2045 point += n++ 16;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2046 point += n++ 4;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2047 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2048 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2049
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2050 while( *n != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2051 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2052 point -= p++ 262144;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2053 point *= 4;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2054 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2055 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2056
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2057 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2058 *pointt = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2059 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2060
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2061 void makepointtable_nuc_octet( int pointt, int n )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2062 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2063 int point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2064 register int *p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2065
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2066 if( *n == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2067 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2068 *pointt = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2069 return;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2070 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2071
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2072 p = n;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2073 point = n++ 16384;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2074 point += n++ 4096;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2075 point += n++ 1024;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2076 point += n++ 256;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2077 point += n++ 64;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2078 point += n++ 16;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2079 point += n++ 4;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2080 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2081 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2082
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2083 while( *n != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2084 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2085 point -= p++ 16384;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2086 point *= 4;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2087 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2088 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2089 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2090 *pointt = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2091 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2092
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2093 void makepointtable_nuc( int pointt, int n )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2094 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2095 int point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2096 register int *p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2097
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2098 if( *n == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2099 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2100 *pointt = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2101 return;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2102 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2103
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2104 p = n;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2105 point = n++ 1024;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2106 point += n++ 256;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2107 point += n++ 64;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2108 point += n++ 16;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2109 point += n++ 4;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2110 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2111 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2112
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2113 while( *n != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2114 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2115 point -= p++ 1024;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2116 point *= 4;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2117 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2118 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2119 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2120 *pointt = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2121 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2122
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2123 void makepointtable( int pointt, int n )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2124 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2125 int point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2126 register int *p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2127
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2128 if( *n == -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2129 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2130 *pointt = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2131 return;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2132 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2133
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2134 p = n;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2135 point = n++ 7776;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2136 point += n++ 1296;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2137 point += n++ 216;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2138 point += n++ 36;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2139 point += n++ 6;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2140 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2141 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2142
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2143 while( *n != END_OF_VEC )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2144 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2145 point -= p++ 7776;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2146 point *= 6;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2147 point += *n++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2148 *pointt++ = point;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2149 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2150 *pointt = END_OF_VEC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2151 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2152
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2153 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2154
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2155 void dndprethread( void arg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2156 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2157 dndprethread_arg_t targ = (dndprethread_arg_t )arg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2158 int njob = targ->njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2159 int thread_no = targ->thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2160 float *selfscore = targ->selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2161 float **mtx = targ->mtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2162 char **seq = targ->seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2163 Jobtable2d *jobpospt = targ->jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2164
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2165 int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2166 float ssi, ssj, bunbo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2167 float mtxv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2168
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2169 if( njob == 1 ) return( NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2170
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2171 while( 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2172 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2173 pthread_mutex_lock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2174 j = jobpospt->j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2175 i = jobpospt->i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2176 j++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2177 // fprintf( stderr, "\n i=%d, j=%d before check\n", i, j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2178 if( j == njob )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2179 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2180 // fprintf( stderr, "\n j = %d, i = %d, njob = %d\n", j, i, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2181 fprintf( stderr, "%4d/%4d (thread %4d), dndpre\r", i+1, njob, thread_no );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2182 i++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2183 j = i + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2184 if( i == njob-1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2185 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2186 // fprintf( stderr, "\n i=%d, njob-1=%d\n", i, njob-1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2187 pthread_mutex_unlock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2188 return( NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2189 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2190 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2191 // fprintf( stderr, "\n i=%d, j=%d after check\n", i, j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2192 jobpospt->j = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2193 jobpospt->i = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2194 pthread_mutex_unlock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2195
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2196 ssi = selfscore[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2197 ssj = selfscore[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2198
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2199 bunbo = MIN( ssi, ssj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2200 if( bunbo == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2201 mtxv = maxdist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2202 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2203 mtxv = maxdist * ( 1.0 - (float)naivepairscore11( seq[i], seq[j], penalty * 10 ) / bunbo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2204 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2205 if( mtxv > 9.0 \|\| mtxv < 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2206 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2207 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2208 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2209 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2210 #else // CHUUI!!! 2012/05/16
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2211 if( mtxv > 2.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2212 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2213 mtxv = 2.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2214 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2215 if( mtxv < 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2216 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2217 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2218 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2219 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2220 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2221 mtx[i][j-i] = mtxv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2222 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2223 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2224
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2225 static void gaplist2alnxthread( void arg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2226 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2227 gaplist2alnxthread_arg_t targ = (gaplist2alnxthread_arg_t )arg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2228 // int thread_no = targ->thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2229 int ncycle = targ->ncycle;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2230 char **seq = targ->seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2231 int *newgaplist = targ->newgaplist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2232 int *posmap = targ->posmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2233 int *jobpospt = targ->jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2234 int tmpseqlen = targ->tmpseqlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2235 int lenfull = targ->lenfull;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2236 char *tmpseq1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2237 int i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2238
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2239 tmpseq1 = AllocateCharVec( tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2240
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2241 while( 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2242 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2243 pthread_mutex_lock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2244 i = *jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2245 if( i == ncycle )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2246 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2247 pthread_mutex_unlock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2248 free( tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2249 return( NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2250 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2251 *jobpospt = i+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2252 pthread_mutex_unlock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2253
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2254 gaplist2alnx( lenfull, tmpseq1, seq[i], newgaplist, posmap, tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2255 // fprintf( stderr, ">%s (iadd=%d)\n%s\n", name[i], iadd, tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2256 strcpy( seq[i], tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2257 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2258 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2259
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2260 static void distancematrixthread( void arg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2261 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2262 distancematrixthread_arg_t targ = (distancematrixthread_arg_t )arg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2263 int thread_no = targ->thread_no;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2264 int njob = targ->njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2265 int norg = targ->norg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2266 int *jobpospt = targ->jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2267 int **pointt = targ->pointt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2268 float **imtx = targ->imtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2269 float **nmtx = targ->nmtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2270 float *selfscore = targ->selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2271 int *nogaplen = targ->nogaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2272
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2273 float lenfac, bunbo, longer, shorter, mtxv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2274 int *table1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2275 int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2276
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2277 while( 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2278 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2279 pthread_mutex_lock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2280 i = *jobpospt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2281 if( i == norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2282 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2283 pthread_mutex_unlock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2284 commonsextet_p( NULL, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2285 return( NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2286 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2287 *jobpospt = i+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2288 pthread_mutex_unlock( targ->mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2289
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2290 table1 = (int *)calloc( tsize, sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2291 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2292 if( i % 100 == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2293 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2294 fprintf( stderr, "\r% 5d / %d (thread %4d)", i+1, norg, thread_no );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2295 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2296 makecompositiontable_p( table1, pointt[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2297
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2298 for( j=i+1; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2299 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2300 mtxv = (float)commonsextet_p( table1, pointt[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2301 if( nogaplen[i] > nogaplen[j] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2302 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2303 longer=(float)nogaplen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2304 shorter=(float)nogaplen[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2305 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2306 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2307 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2308 longer=(float)nogaplen[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2309 shorter=(float)nogaplen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2310 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2311 lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2312 bunbo = MIN( selfscore[i], selfscore[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2313
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2314 if( j < norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2315 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2316 if( bunbo == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2317 imtx[i][j-i] = maxdist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2318 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2319 imtx[i][j-i] = maxdist * ( 1.0 - mtxv / bunbo ) * lenfac;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2320
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2321 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2322 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2323 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2324 if( bunbo == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2325 nmtx[i][j-norg] = maxdist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2326 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2327 nmtx[i][j-norg] = maxdist * ( 1.0 - mtxv / bunbo ) * lenfac;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2328 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2329 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2330 free( table1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2331
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2332 // for( j=i+1; j<norg; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2333 // imtx[i][j-i] = (float)commonsextet_p( table1, pointt[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2334 // for( j=norg; j<njob; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2335 // nmtx[i][j-norg] = (float)commonsextet_p( table1, pointt[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2336 // free( table1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2337 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2338 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2339 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2340
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2341
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2342 void ktupledistancematrix( int nseq, int norg, int nlenmax, char seq, char name, float imtx, float nmtx )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2343 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2344 char *tmpseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2345 int *grpseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2346 int **pointt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2347 int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2348 int *nogaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2349 int *table1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2350 float lenfac, bunbo, longer, shorter, mtxv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2351 float *selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2352 selfscore = AllocateFloatVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2353
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2354 fprintf( stderr, "\n\nMaking a distance matrix ..\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2355 fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2356
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2357 tmpseq = AllocateCharVec( nlenmax+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2358 grpseq = AllocateIntVec( nlenmax+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2359 pointt = AllocateIntMtx( nseq, nlenmax+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2360 nogaplen = AllocateIntVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2361
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2362 if( dorp == 'd' ) tsize = (int)pow( 4, tuplesize );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2363 else tsize = (int)pow( 6, 6 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2364
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2365 if( dorp == 'd' && tuplesize == 6 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2366 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2367 lenfaca = D6LENFACA;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2368 lenfacb = D6LENFACB;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2369 lenfacc = D6LENFACC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2370 lenfacd = D6LENFACD;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2371 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2372 else if( dorp == 'd' && tuplesize == 10 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2373 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2374 lenfaca = D10LENFACA;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2375 lenfacb = D10LENFACB;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2376 lenfacc = D10LENFACC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2377 lenfacd = D10LENFACD;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2378 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2379 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2380 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2381 lenfaca = PLENFACA;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2382 lenfacb = PLENFACB;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2383 lenfacc = PLENFACC;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2384 lenfacd = PLENFACD;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2385 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2386
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2387 maxl = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2388 for( i=0; i<nseq; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2389 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2390 gappick0( tmpseq, seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2391 nogaplen[i] = strlen( tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2392 if( nogaplen[i] < 6 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2393 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2394 // fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nogaplen[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2395 // fprintf( stderr, "Please use mafft-ginsi, mafft-linsi or mafft-ginsi\n\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2396 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2397 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2398 if( nogaplen[i] > maxl ) maxl = nogaplen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2399 if( dorp == 'd' ) /* nuc */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2400 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2401 seq_grp_nuc( grpseq, tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2402 // makepointtable_nuc( pointt[i], grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2403 // makepointtable_nuc_octet( pointt[i], grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2404 if( tuplesize == 10 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2405 makepointtable_nuc_dectet( pointt[i], grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2406 else if( tuplesize == 6 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2407 makepointtable_nuc( pointt[i], grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2408 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2409 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2410 fprintf( stderr, "tuplesize=%d: not supported\n", tuplesize );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2411 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2412 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2413 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2414 else /* amino */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2415 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2416 seq_grp( grpseq, tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2417 makepointtable( pointt[i], grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2418 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2419
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2420 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2421 if( nunknown ) fprintf( stderr, "\nThere are %d ambiguous characters\n", nunknown );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2422
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2423 for( i=0; i<nseq; i++ ) // serial de jubun
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2424 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2425 table1 = (int *)calloc( tsize, sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2426 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2427 makecompositiontable_p( table1, pointt[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2428
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2429 selfscore[i] = (float)commonsextet_p( table1, pointt[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2430 free( table1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2431 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2432
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2433 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2434 if( nthread > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2435 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2436 distancematrixthread_arg_t *targ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2437 int jobpos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2438 pthread_t *handle;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2439 pthread_mutex_t mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2440
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2441 jobpos = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2442 targ = calloc( nthread, sizeof( distancematrixthread_arg_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2443 handle = calloc( nthread, sizeof( pthread_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2444 pthread_mutex_init( &mutex, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2445
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2446 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2447 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2448 targ[i].thread_no = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2449 targ[i].njob = nseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2450 targ[i].norg = norg;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2451 targ[i].jobpospt = &jobpos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2452 targ[i].pointt = pointt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2453 targ[i].imtx = imtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2454 targ[i].nmtx = nmtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2455 targ[i].selfscore = selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2456 targ[i].nogaplen = nogaplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2457 targ[i].mutex = &mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2458
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2459 pthread_create( handle+i, NULL, distancematrixthread, (void *)(targ+i) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2460 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2461
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2462 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2463 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2464 pthread_join( handle[i], NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2465 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2466 pthread_mutex_destroy( &mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2467 free( handle );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2468 free( targ );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2469
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2470 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2471 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2472 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2473 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2474 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2475 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2476 table1 = (int *)calloc( tsize, sizeof( int ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2477 if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2478 if( i % 100 == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2479 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2480 fprintf( stderr, "\r% 5d / %d", i+1, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2481 fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2482 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2483 makecompositiontable_p( table1, pointt[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2484
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2485 for( j=i+1; j<nseq; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2486 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2487 mtxv = (float)commonsextet_p( table1, pointt[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2488 if( nogaplen[i] > nogaplen[j] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2489 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2490 longer=(float)nogaplen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2491 shorter=(float)nogaplen[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2492 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2493 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2494 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2495 longer=(float)nogaplen[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2496 shorter=(float)nogaplen[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2497 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2498 lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2499 bunbo = MIN( selfscore[i], selfscore[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2500
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2501 if( j < norg )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2502 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2503 if( bunbo == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2504 imtx[i][j-i] = maxdist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2505 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2506 imtx[i][j-i] = maxdist * ( 1.0 - mtxv / bunbo ) * lenfac;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2507 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2508 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2509 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2510 if( bunbo == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2511 nmtx[i][j-norg] = maxdist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2512 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2513 nmtx[i][j-norg] = maxdist * ( 1.0 - mtxv / bunbo ) * lenfac;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2514 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2515 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2516 free( table1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2517 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2518 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2519
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2520 fprintf( stderr, "\ndone.\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2521 fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2522
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2523 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2524 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2525 for( j=i+1; j<norg; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2526 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2527
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2528 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2529 for( j=norg; j<nseq; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2530 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2531 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2532 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2533 free( grpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2534 free( tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2535 FreeIntMtx( pointt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2536 free( nogaplen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2537 free( selfscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2538
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2539 #if 0 // writehat2 wo kakinaosu
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2540 if( distout )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2541 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2542 hat2p = fopen( "hat2", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2543 WriteFloatHat2_pointer_halfmtx( hat2p, nseq, name, mtx );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2544 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2545 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2546 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2547 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2548
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2549 void dndpre( int nseq, char seq, float mtx ) // not used yet
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2550 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2551 int i, j, ilim;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2552 float *selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2553 float mtxv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2554 float ssi, ssj, bunbo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2555
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2556 selfscore = AllocateFloatVec( nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2557
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2558 for( i=0; i<nseq; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2559 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2560 selfscore[i] = (float)naivepairscore11( seq[i], seq[i], 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2561 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2562 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2563 if( nthread > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2564 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2565 dndprethread_arg_t *targ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2566 Jobtable2d jobpos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2567 pthread_t *handle;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2568 pthread_mutex_t mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2569
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2570 jobpos.i = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2571 jobpos.j = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2572
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2573 targ = calloc( nthread, sizeof( dndprethread_arg_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2574 handle = calloc( nthread, sizeof( pthread_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2575 pthread_mutex_init( &mutex, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2576
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2577 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2578 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2579 targ[i].thread_no = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2580 targ[i].njob = nseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2581 targ[i].selfscore = selfscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2582 targ[i].mtx = mtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2583 targ[i].seq = seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2584 targ[i].jobpospt = &jobpos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2585 targ[i].mutex = &mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2586
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2587 pthread_create( handle+i, NULL, dndprethread, (void *)(targ+i) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2588 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2589
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2590 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2591 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2592 pthread_join( handle[i], NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2593 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2594 pthread_mutex_destroy( &mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2595
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2596 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2597 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2598 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2599 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2600 ilim = nseq-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2601 for( i=0; i<ilim; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2602 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2603 ssi = selfscore[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2604 fprintf( stderr, "%4d/%4d\r", i+1, nseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2605
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2606 for( j=i+1; j<nseq; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2607 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2608 ssj = selfscore[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2609 bunbo = MIN( ssi, ssj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2610 if( bunbo == 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2611 mtxv = maxdist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2612 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2613 mtxv = maxdist * ( 1.0 - (float)naivepairscore11( seq[i], seq[j], penalty * 10 ) / bunbo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2614
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2615 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2616 if( mtxv > 9.0 \|\| mtxv < 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2617 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2618 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2619 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2620 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2621 #else // CHUUI!!! 2012/05/16
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2622 if( mtxv > 2.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2623 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2624 mtxv = 2.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2625 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2626 if( mtxv < 0.0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2627 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2628 fprintf( stderr, "Distance %d-%d is strange, %f.\n", i, j, mtxv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2629 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2630 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2631 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2632 mtx[i][j-i] = mtxv;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2633 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2634 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2635 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2636
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2637 #if TEST
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2638 for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2639 fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2640 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2641 free( selfscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2642
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2643 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2644
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2645 int main( int argc, char *argv[] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2646 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2647 static int *nlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2648 static char name, seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2649 static char **tmpseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2650 static char *tmpseq1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2651 // static char check1, check2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2652 static float iscore, iscore_kozo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2653 static double eff_kozo, eff_kozo_mapped = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2654 int i, j, f, ien;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2655 int iadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2656 static int ***topol_kozo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2657 Treedep *dep;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2658 static float **len_kozo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2659 FILE *prep;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2660 FILE *infp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2661 FILE *hat2p;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2662 int alignmentlength;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2663 char c;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2664 int alloclen, fullseqlen, tmplen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2665 LocalHom **localhomtable = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2666 static char *kozoarivec;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2667 int nkozo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2668 int njobc, norg, lenfull;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2669 int **newgaplist_o;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2670 int *newgaplist_compact;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2671 int **follower;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2672 int *follows;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2673 int *istherenewgap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2674 int zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2675 int *posmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2676 int *ordertable;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2677 FILE *orderfp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2678 int tmpseqlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2679 Blocktorealign *realign;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2680 RNApair ***singlerna;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2681 int ***topol;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2682 float **len;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2683 float iscoreo, nscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2684 FILE *fp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2685 Addtree *addtree;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2686
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2687
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2688 arguments( argc, argv );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2689 #ifndef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2690 nthread = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2691 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2692
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2693 if( fastathreshold < 0.0001 ) constraint = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2694
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2695 if( inputfile )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2696 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2697 infp = fopen( inputfile, "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2698 if( !infp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2699 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2700 fprintf( stderr, "Cannot open %s\n", inputfile );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2701 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2702 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2703 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2704 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2705 infp = stdin;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2706
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2707 getnumlen( infp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2708 rewind( infp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2709
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2710
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2711 nkozo = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2712
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2713 if( njob < 2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2714 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2715 fprintf( stderr, "At least 2 sequences should be input!\n"
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2716 "Only %d sequence found.\n", njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2717 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2718 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2719
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2720 norg = njob-nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2721 njobc = norg+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2722 fprintf( stderr, "norg = %d\n", norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2723 fprintf( stderr, "njobc = %d\n", njobc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2724 if( norg > 1000 \|\| nadd > 1000 ) use_fft = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2725
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2726 fullseqlen = alloclen = nlenmax*4+1; //chuui!
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2727 seq = AllocateCharMtx( njob, alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2728
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2729 name = AllocateCharMtx( njob, B+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2730 nlen = AllocateIntVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2731
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2732
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2733 if( multidist \|\| tuplesize > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2734 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2735 iscore = AllocateFloatHalfMtx( norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2736 nscore = AllocateFloatMtx( norg, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2737 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2738 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2739 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2740 iscore = AllocateFloatHalfMtx( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2741 nscore = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2742 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2743
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2744 kozoarivec = AllocateCharVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2745
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2746
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2747 ordertable = AllocateIntVec( norg+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2748
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2749
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2750 if( constraint )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2751 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2752 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2753 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2754 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2755 localhomtable = (LocalHom *)calloc( norg, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2756 for( i=0; i<norg; i++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2757 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2758 localhomtable[i] = (LocalHom *)calloc( nadd, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2759 for( j=0; j<nadd; j++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2760 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2761 localhomtable[i][j].start1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2762 localhomtable[i][j].end1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2763 localhomtable[i][j].start2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2764 localhomtable[i][j].end2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2765 localhomtable[i][j].overlapaa = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2766 localhomtable[i][j].opt = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2767 localhomtable[i][j].importance = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2768 localhomtable[i][j].next = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2769 localhomtable[i][j].korh = 'h';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2770 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2771 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2772 // localhomtable = (LocalHom *)calloc( norg+nadd, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2773 // for( i=norg; i<norg+nadd; i++) // hontou ha iranai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2774 // {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2775 // localhomtable[i] = (LocalHom *)calloc( norg, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2776 // for( j=0; j<norg; j++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2777 // {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2778 // localhomtable[i][j].start1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2779 // localhomtable[i][j].end1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2780 // localhomtable[i][j].start2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2781 // localhomtable[i][j].end2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2782 // localhomtable[i][j].overlapaa = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2783 // localhomtable[i][j].opt = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2784 // localhomtable[i][j].importance = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2785 // localhomtable[i][j].next = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2786 // localhomtable[i][j].korh = 'h';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2787 // }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2788 // }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2789 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2790 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2791 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2792 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2793 localhomtable = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2794 for( i=0; i<njob; i++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2795 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2796 localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2797 for( j=0; j<njob; j++)
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2798 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2799 localhomtable[i][j].start1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2800 localhomtable[i][j].end1 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2801 localhomtable[i][j].start2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2802 localhomtable[i][j].end2 = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2803 localhomtable[i][j].overlapaa = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2804 localhomtable[i][j].opt = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2805 localhomtable[i][j].importance = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2806 localhomtable[i][j].next = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2807 localhomtable[i][j].korh = 'h';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2808 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2809 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2810 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2811
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2812 fprintf( stderr, "Loading 'hat3' ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2813 prep = fopen( "hat3", "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2814 if( prep == NULL ) ErrorExit( "Make hat3." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2815 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2816 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2817 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2818 // readlocalhomtable_two( prep, norg, nadd, localhomtable, localhomtable+norg, kozoarivec );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2819 readlocalhomtable_one( prep, norg, nadd, localhomtable, kozoarivec );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2820 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2821 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2822 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2823 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2824 readlocalhomtable( prep, njob, localhomtable, kozoarivec );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2825 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2826
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2827 fclose( prep );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2828 fprintf( stderr, "\ndone.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2829
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2830
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2831 nkozo = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2832 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2833 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2834 // fprintf( stderr, "kozoarivec[%d] = %d\n", i, kozoarivec[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2835 if( kozoarivec[i] ) nkozo++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2836 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2837 if( nkozo )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2838 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2839 topol_kozo = AllocateIntCub( nkozo, 2, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2840 len_kozo = AllocateFloatMtx( nkozo, 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2841 iscore_kozo = AllocateFloatHalfMtx( nkozo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2842 eff_kozo = AllocateDoubleVec( nkozo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2843 eff_kozo_mapped = AllocateDoubleVec( njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2844 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2845
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2846
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2847 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2848 // outlocalhom_part( localhomtable, norg, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2849 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2850 // outlocalhom( localhomtable, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2851 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2852
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2853 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2854 fprintf( stderr, "Extending localhom ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2855 extendlocalhom2( njob, localhomtable );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2856 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2857 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2858 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2859
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2860 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2861 readData( infp, name, nlen, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2862 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2863 readData_pointer( infp, name, nlen, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2864 fclose( infp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2865 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2866
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2867 constants( njob, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2868
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2869 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2870 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2871 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2872
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2873 initSignalSM();
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2874
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2875 initFiles();
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2876
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2877 // WriteOptions( trap_g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2878
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2879 c = seqcheck( seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2880 if( c )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2881 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2882 fprintf( stderr, "Illegal character %c\n", c );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2883 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2884 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2885
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2886 alignmentlength = strlen( seq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2887 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2888 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2889 if( alignmentlength != strlen( seq[i] ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2890 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2891 fprintf( stderr, "#################################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2892 fprintf( stderr, "# ERROR! #\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2893 fprintf( stderr, "# The original%4d sequences must be aligned #\n", njob-nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2894 fprintf( stderr, "#################################################################################\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2895 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2896 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2897 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2898 if( addprofile )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2899 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2900 fprintf( stderr, "Not supported!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2901 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2902 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2903
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2904 if( tuplesize > 0 ) // if mtx is internally computed
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2905 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2906 if( multidist == 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2907 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2908 ktupledistancematrix( njob, norg, nlenmax, seq, name, iscore, nscore ); // iscore ha muda.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2909
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2910 // hat2p = fopen( "hat2-1", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2911 // WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2912 // fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2913
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2914 dndpre( norg, seq, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2915 // fprintf( stderr, "Loading 'hat2i' (aligned sequences) ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2916 // prep = fopen( "hat2i", "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2917 // if( prep == NULL ) ErrorExit( "Make hat2i." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2918 // readhat2_floathalf_pointer( prep, njob-nadd, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2919 // fclose( prep );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2920 // fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2921
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2922 // hat2p = fopen( "hat2-2", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2923 // WriteFloatHat2_pointer_halfmtx( hat2p, norg, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2924 // fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2925 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2926 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2927 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2928 ktupledistancematrix( njob, norg, nlenmax, seq, name, iscore, nscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2929 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2930 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2931 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2932 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2933 if( multidist == 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2934 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2935 fprintf( stderr, "Loading 'hat2n' (aligned sequences - new sequences) ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2936 prep = fopen( "hat2n", "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2937 if( prep == NULL ) ErrorExit( "Make hat2n." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2938 readhat2_floathalf_part_pointer( prep, njob, nadd, name, nscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2939 fclose( prep );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2940 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2941
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2942 fprintf( stderr, "Loading 'hat2i' (aligned sequences) ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2943 prep = fopen( "hat2i", "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2944 if( prep == NULL ) ErrorExit( "Make hat2i." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2945 readhat2_floathalf_pointer( prep, njob-nadd, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2946 fclose( prep );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2947 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2948 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2949 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2950 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2951 fprintf( stderr, "Loading 'hat2' ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2952 prep = fopen( "hat2", "r" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2953 if( prep == NULL ) ErrorExit( "Make hat2." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2954 readhat2_floathalf_pointer( prep, njob, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2955 fclose( prep );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2956 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2957 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2958 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2959
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2960 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2961 if( distout )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2962 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2963 fprintf( stderr, "Writing distances between new sequences and existing msa.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2964 hat2p = fopen( "hat2", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2965 if( multidist \|\| tuplesize > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2966 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2967 for( iadd=0; iadd<nadd; iadd++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2968 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2969 fprintf( hat2p, "Distance between new sequence %d and %d sequences in existing msa\n", iadd+1, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2970 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2971 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2972 fprintf( hat2p, "%5.3f ", nscore[i][iadd] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2973 if( (i+1) % 12 == 0 ) fprintf( hat2p, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2974 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2975 fprintf( hat2p, "\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2976 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2977 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2978 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2979 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2980 for( iadd=0; iadd<nadd; iadd++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2981 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2982 fprintf( hat2p, "Distance between new sequence %d and %d sequences in existing msa\n", iadd+1, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2983 for( i=0; i<norg; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2984 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2985 fprintf( hat2p, "%5.3f ", iscore[i][norg+iadd-i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2986 if( (i+1) % 12 == 0 ) fprintf( hat2p, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2987 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2988 fprintf( hat2p, "\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2989 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2990 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2991 fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2992 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2993 // hat2p = fopen( "hat2", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2994 // WriteFloatHat2_pointer_halfmtx( hat2p, norg, name, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2995 // fclose( hat2p );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2996 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2997 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2998 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2999
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3001 singlerna = NULL;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3002
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3003 commongappick( norg, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3004
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3005 lenfull = strlen( seq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3006
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3007 // newgaplist_o = AllocateIntMtx( nadd, alloclen ); //ookisugi
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3008 newgaplist_o = AllocateIntMtx( nadd, lenfull*2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3009 newgaplist_compact = AllocateIntVec( lenfull*2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3010 istherenewgap = AllocateIntVec( nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3011 follower = AllocateIntMtx( norg, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3012 for( i=0; i<norg; i++ ) follower[i][0] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3013 follows = AllocateIntVec( nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3014
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3015 dep = (Treedep *)calloc( norg, sizeof( Treedep ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3016 topol = AllocateIntCub( norg, 2, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3017 len = AllocateFloatMtx( norg, 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3018 // iscoreo = AllocateFloatHalfMtx( norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3019 mtxcpy( norg, norg, &iscoreo, iscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3020
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3021 if( treeout )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3022 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3023 addtree = (Addtree *)calloc( nadd, sizeof( Addtree ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3024 if( !addtree )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3025 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3026 fprintf( stderr, "Cannot allocate addtree\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3027 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3028 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3029 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3030
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3031
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3032 // nlim = norg-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3033 // for( i=0; i<nlim; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3034 // {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3035 // fptc = iscoreo[i]+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3036 // fpt = iscore[i]+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3037 // j = norg-i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3038 // while( j-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3039 // fptc++ = fpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3040 //// for( j=i+1; j<norg; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3041 //// iscoreo[i][j-i] = iscore[i][j-i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3042 // }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3043
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3044 // fprintf( stderr, "building a tree.." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3045 if( treein )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3046 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3047 reporterr( "Loading a tree ... " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3048 loadtop( norg, iscoreo, topol, len, name, NULL, dep ); // nogaplen?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3049 reporterr( "\ndone.\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3050 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3051 else if( treeout )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3052 fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( norg, iscoreo, topol, len, name, nlen, dep, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3053 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3054 fixed_musclesupg_float_realloc_nobk_halfmtx( norg, iscoreo, topol, len, dep, 0, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3055 // fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3056
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3057 if( norg > 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3058 cnctintvec( ordertable, topol[norg-2][0], topol[norg-2][1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3059 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3060 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3061 ordertable[0] = 0; ordertable[1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3062 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3063 FreeFloatHalfMtx( iscoreo, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3064
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3065 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3066 if( nthread )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3067 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3068 pthread_t *handle;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3069 pthread_mutex_t mutex_counter;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3070 thread_arg_t *targ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3071 int *iaddsharept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3072
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3073 targ = calloc( nthread, sizeof( thread_arg_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3074 handle = calloc( nthread, sizeof( pthread_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3075 pthread_mutex_init( &mutex_counter, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3076 iaddsharept = calloc( 1, sizeof(int) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3077 *iaddsharept = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3078
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3079 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3080 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3081 targ[i].thread_no = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3082 targ[i].follows = follows;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3083 targ[i].njob = njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3084 targ[i].nadd = nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3085 targ[i].nlen = nlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3086 targ[i].name = name;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3087 targ[i].seq = seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3088 targ[i].localhomtable = localhomtable;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3089 targ[i].iscore = iscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3090 targ[i].nscore = nscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3091 targ[i].istherenewgap = istherenewgap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3092 targ[i].newgaplist = newgaplist_o;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3093 targ[i].singlerna = singlerna;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3094 targ[i].eff_kozo_mapped = eff_kozo_mapped;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3095 targ[i].alloclen = alloclen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3096 targ[i].iaddshare = iaddsharept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3097 targ[i].dep = dep;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3098 targ[i].topol = topol;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3099 targ[i].len = len;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3100 targ[i].addtree = addtree;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3101 targ[i].mutex_counter = &mutex_counter;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3102 pthread_create( handle+i, NULL, addsinglethread, (void *)(targ+i) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3103 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3104 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3105 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3106 pthread_join( handle[i], NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3107 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3108 pthread_mutex_destroy( &mutex_counter );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3109 free( handle );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3110 free( targ );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3111 free( iaddsharept );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3112 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3113 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3114 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3115 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3116 thread_arg_t *targ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3117 targ = calloc( 1, sizeof( thread_arg_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3118 targ[0].follows = follows;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3119 targ[0].njob = njob;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3120 targ[0].nadd = nadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3121 targ[0].nlen = nlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3122 targ[0].name = name;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3123 targ[0].seq = seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3124 targ[0].localhomtable = localhomtable;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3125 targ[0].iscore = iscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3126 targ[0].nscore = nscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3127 targ[0].istherenewgap = istherenewgap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3128 targ[0].newgaplist = newgaplist_o;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3129 targ[0].singlerna = singlerna;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3130 targ[0].eff_kozo_mapped = eff_kozo_mapped;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3131 targ[0].alloclen = alloclen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3132 targ[0].dep = dep;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3133 targ[0].topol = topol;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3134 targ[0].len = len;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3135 targ[0].addtree = addtree;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3136 addsinglethread( targ );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3137 free( targ );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3138 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3139 free( dep );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3140 FreeFloatMtx( len );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3141 if( multidist \|\| tuplesize > 0 ) FreeFloatMtx( nscore );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3142
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3143 // for( i=0; i<nadd; i++ ) fprintf( stdout, ">%s (%d) \n%s\n", name[norg+i], norg+i, seq[norg+i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3144
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3145 if( treeout )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3146 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3147 fp = fopen( "infile.tree", "a" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3148 if( fp == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3149 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3150 fprintf( stderr, "File error!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3151 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3152 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3153 for( i=0; i<nadd; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3154 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3155 fprintf( fp, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3156 fprintf( fp, "%8d: %s\n", norg+i+1, name[norg+i]+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3157 fprintf( fp, " nearest sequence: %d\n", addtree[i].nearest + 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3158 fprintf( fp, " approximate distance: %f\n", addtree[i].dist1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3159 fprintf( fp, " sister group: %s\n", addtree[i].neighbors );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3160 fprintf( fp, " approximate distance: %f\n", addtree[i].dist2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3161 free( addtree[i].neighbors );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3162 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3163 fclose( fp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3164 free( addtree );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3165 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3166
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3167 for( iadd=0; iadd<nadd; iadd++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3168 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3169 f = follows[iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3170 for( i=0; follower[f][i]!=-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3171 ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3172 if( !(follower[f] = realloc( follower[f], (i+2)*sizeof(int) ) ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3173 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3174 fprintf( stderr, "Cannot reallocate follower[]" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3175 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3176 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3177 follower[f][i] = iadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3178 follower[f][i+1] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3179 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3180 fprintf( stderr, "\nfollowers of %d = ", f );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3181 for( i=0; follower[f][i]!=-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3182 fprintf( stderr, "%d ", follower[f][i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3183 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3184 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3185 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3186
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3187 orderfp = fopen( "order", "w" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3188 if( !orderfp )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3189 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3190 fprintf( stderr, "Cannot open 'order'\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3191 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3192 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3193 for( i=0; ordertable[i]!=-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3194 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3195 fprintf( orderfp, "%d\n", ordertable[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3196 // for( j=0; follower[i][j]!=-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3197 // fprintf( orderfp, "%d\n", follower[i][j]+norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3198 for( j=0; follower[ordertable[i]][j]!=-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3199 fprintf( orderfp, "%d\n", follower[ordertable[i]][j]+norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3200 // fprintf( orderfp, "%d -> %d\n", follower[i][j]+norg, i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3201 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3202 fclose( orderfp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3203
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3204 posmap = AllocateIntVec( lenfull+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3205 realign = calloc( lenfull+2, sizeof( Blocktorealign ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3206 for( i=0; i<lenfull+1; i++ ) posmap[i] = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3207 for( i=0; i<lenfull+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3208 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3209 realign[i].nnewres = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3210 realign[i].start = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3211 realign[i].end = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3212 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3213
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3214 fprintf( stderr, "\n\nCombining ..\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3215 fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3216 tmpseqlen = alloclen * 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3217 tmpseq = AllocateCharMtx( 1, tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3218 // check1 = AllocateCharVec( tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3219 // check2 = AllocateCharVec( tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3220 // gappick0( check2, seq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3221 for( iadd=0; iadd<nadd; iadd++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3222 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3223 // fprintf( stderr, "%d / %d\r", iadd, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3224 fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3225
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3226 // fprintf( stderr, "\niadd == %d\n", iadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3227 makegaplistcompact( lenfull, posmap, newgaplist_compact, newgaplist_o[iadd] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3228 if( iadd == 0 \|\| istherenewgap[iadd] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3229 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3230 tmpseq1 = tmpseq[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3231 // gaplist2alnx( lenfull, tmpseq1, seq[0], newgaplist_o[iadd], posmap, tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3232 gaplist2alnx( lenfull, tmpseq1, seq[0], newgaplist_compact, posmap, tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3233 // fprintf( stderr, "len = %d ? %d\n", strlen( tmpseq1 ), alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3234 if( ( tmplen = strlen( tmpseq1 ) ) >= fullseqlen )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3235 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3236 fullseqlen = tmplen * 2+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3237 // fprintf( stderr, "Length over!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3238 // fprintf( stderr, "strlen(tmpseq1)=%d\n", (int)strlen( tmpseq1 ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3239 fprintf( stderr, "reallocating..." );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3240 // fprintf( stderr, "alloclen=%d\n", alloclen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3241 // fprintf( stderr, "Please recompile!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3242 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3243 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3244 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3245 seq[i] = realloc( seq[i], fullseqlen * sizeof( char ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3246 if( !seq[i] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3247 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3248 fprintf( stderr, "Cannot reallocate seq[][]\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3249 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3250 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3251 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3252 fprintf( stderr, "done.\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3253 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3254 strcpy( seq[0], tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3255
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3256 ien = norg+iadd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3257 #ifdef enablemultithread
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3258 if( nthread > 0 && ien > 500 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3259 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3260 gaplist2alnxthread_arg_t *targ;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3261 int jobpos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3262 pthread_t *handle;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3263 pthread_mutex_t mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3264 fprintf( stderr, "%d / %d (threads %d-%d)\r", iadd, nadd, 0, nthread );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3265
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3266 targ = calloc( nthread, sizeof( gaplist2alnxthread_arg_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3267 handle = calloc( nthread, sizeof( pthread_t ) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3268 pthread_mutex_init( &mutex, NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3269 jobpos = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3270 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3271 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3272 // targ[i].thread_no = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3273 targ[i].ncycle = ien;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3274 targ[i].jobpospt = &jobpos;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3275 targ[i].tmpseqlen = tmpseqlen;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3276 targ[i].lenfull = lenfull;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3277 targ[i].seq = seq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3278 // targ[i].newgaplist = newgaplist_o[iadd];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3279 targ[i].newgaplist = newgaplist_compact;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3280 targ[i].posmap = posmap;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3281 targ[i].mutex = &mutex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3282
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3283 pthread_create( handle+i, NULL, gaplist2alnxthread, (void *)(targ+i) );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3284 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3285 for( i=0; i<nthread; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3286 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3287 pthread_join( handle[i], NULL );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3288 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3289 pthread_mutex_destroy( &mutex );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3290 free( handle );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3291 free( targ );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3292 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3293 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3294 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3295 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3296 fprintf( stderr, "%d / %d\r", iadd, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3297 for( i=1; i<ien; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3298 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3299 tmpseq1 = tmpseq[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3300 if( i == 1 ) fprintf( stderr, " %d / %d\r", iadd, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3301 // gaplist2alnx( lenfull, tmpseq1, seq[i], newgaplist_o[iadd], posmap, tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3302 gaplist2alnx( lenfull, tmpseq1, seq[i], newgaplist_compact, posmap, tmpseqlen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3303 // fprintf( stderr, ">%s (iadd=%d)\n%s\n", name[i], iadd, tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3304 strcpy( seq[i], tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3305 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3306 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3307 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3308 tmpseq1 = tmpseq[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3309 // insertgapsbyotherfragments_simple( lenfull, tmpseq1, seq[norg+iadd], newgaplist_o[iadd], posmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3310 insertgapsbyotherfragments_compact( lenfull, tmpseq1, seq[norg+iadd], newgaplist_o[iadd], posmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3311 // fprintf( stderr, "%d = %s\n", iadd, tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3312 eq2dash( tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3313 strcpy( seq[norg+iadd], tmpseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3314
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3315 // adjustposmap( lenfull, posmap, newgaplist_o[iadd] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3316 adjustposmap( lenfull, posmap, newgaplist_compact );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3317 countnewres( lenfull, realign, posmap, newgaplist_o[iadd] ); // muda?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3318 // countnewres( lenfull, realign, posmap, newgaplist_compact ); // muda?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3319
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3320 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3321 fprintf( stderr, "\r done. \n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3322
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3323 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3324 for( i=0; i<njob; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3325 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3326 fprintf( stdout, ">%s\n", name[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3327 fprintf( stdout, "%s\n", seq[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3328 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3329 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3330
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3331 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3332 fprintf( stderr, "realign[].nnewres = " );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3333 for( i=0; i<lenfull+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3334 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3335 fprintf( stderr, "%d ", realign[i].nnewres );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3336 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3337 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3338 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3339
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3340 for( i=0; i<lenfull+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3341 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3342 if( realign[i].nnewres > 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3343 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3344 // fprintf( stderr, "i=%d: %d-%d\n", i, realign[i].start, realign[i].end );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3345 fprintf( stderr, "\rRealigning %d/%d \r", i, lenfull );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3346 // zure = dorealignment_compact( realign+i, seq, &fullseqlen, norg );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3347 // zure = dorealignment_order( realign+i, seq, &fullseqlen, norg, ordertable, follows );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3348 zure = dorealignment_tree( realign+i, seq, &fullseqlen, norg, topol, follows );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3349 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3350 gappick0( check1, seq[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3351 fprintf( stderr, "check1 = %s\n", check1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3352 if( strcmp( check1, check2 ) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3353 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3354 fprintf( stderr, "CHANGED!!!!!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3355 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3356 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3357 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3358 for( j=i+1; j<lenfull+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3359 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3360 if( realign[j].nnewres )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3361 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3362 realign[j].start -= zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3363 realign[j].end -= zure;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3364 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3365 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3366 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3367 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3368 FreeIntCub( topol );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3369 fprintf( stderr, "\r done. \n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3370
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3371 fflush( stderr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3372
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3373
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3374 FreeIntMtx( newgaplist_o );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3375 FreeIntVec( newgaplist_compact );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3376 FreeIntVec( posmap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3377 free( realign );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3378 free( istherenewgap );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3379 FreeIntMtx( follower );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3380 free( follows );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3381 free( ordertable );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3382 FreeCharMtx( tmpseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3383
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3384
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3385 writeData_pointer( prep_g, njob, name, nlen, seq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3386 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3387 writeData( stdout, njob, name, nlen, bseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3388 writePre( njob, name, nlen, bseq, !contin );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3389 writeData_pointer( prep_g, njob, name, nlen, aseq );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3390 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3391 #if IODEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3392 fprintf( stderr, "OSHIMAI\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3393 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3394
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3395 #if SMALLMEMORY
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3396 if( multidist )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3397 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3398 // if( constraint ) FreeLocalHomTable_two( localhomtable, norg, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3399 if( constraint ) FreeLocalHomTable_one( localhomtable, norg, nadd );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3400 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3401 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3402 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3403 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3404 if( constraint ) FreeLocalHomTable( localhomtable, njob );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3405 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3406
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3407 SHOWVERSION;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3408 return( 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3409 }

Mercurial > repos > nick > duplex

annotate mafft/core/addsingle.c @ 18:e4d75f9efb90 draft