duplex: mafft/core/Lalignmm.c annotate

annotate mafft/core/Lalignmm.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 #include "dp.h"
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	3
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	4 #define MEMSAVE 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	5
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	6 #define DEBUG 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	7 #define USE_PENALTY_EX 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	8 #define STOREWM 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	9
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	10 #define DPTANNI 10
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	11
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	12 #define LOCAL 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	13
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	14 static int reccycle = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	15
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	16 static float localthr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	17
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	18 static void match_ribosum( float match, float cpmx1, float cpmx2, int i1, int lgth2, float floatwork, int *intwork, int initialize )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	19 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	20 int j, k, l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	21 float scarr[38];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	22 float **cpmxpd = floatwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	23 int **cpmxpdn = intwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	24 int count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	25 float *matchpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	26 float **cpmxpdpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	27 int **cpmxpdnpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	28 int cpkd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	29
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	30 if( initialize )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	31 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	32 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	33 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	34 count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	35 for( l=0; l<37; l++ )
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 if( cpmx2[j][l] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	38 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	39 cpmxpd[j][count] = cpmx2[j][l];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	40 cpmxpdn[j][count] = l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	41 count++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	42 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	43 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	44 cpmxpdn[j][count] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	45 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	46 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	47
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	48 for( l=0; l<37; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	49 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	50 scarr[l] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	51 for( k=0; k<37; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	52 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	53 scarr[l] += ribosumdis[k][l] * cpmx1[i1][k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	54 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	55 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	56 #if 0 /* ��Ȥ��Ȥ��floatwork�Υ��Ȥ�դˤ�� */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	57 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	58 float fpt, fptpt, fpt2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	59 int ipt, *iptpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	60 fpt2 = match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	61 iptpt = cpmxpdn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	62 fptpt = cpmxpd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	63 while( lgth2-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	64 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	65 *fpt2 = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	66 ipt=iptpt,fpt=fptpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	67 while( *ipt > -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	68 fpt2 += scarr[ipt++] * *fpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	69 fpt2++,iptpt++,fptpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	70 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	71 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	72 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	73 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	74 match[j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	75 for( k=0; cpmxpdn[j][k]>-1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	76 match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	77 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	78 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	79 matchpt = match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	80 cpmxpdnpt = cpmxpdn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	81 cpmxpdpt = cpmxpd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	82 while( lgth2-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	83 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	84 *matchpt = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	85 for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	86 matchpt += scarr[cpkd] (*cpmxpdpt)[k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	87 matchpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	88 cpmxpdnpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	89 cpmxpdpt++;
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 #endif
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	94 static void match_calc( float match, float cpmx1, float cpmx2, int i1, int lgth2, float floatwork, int *intwork, int initialize )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	95 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	96 int j, k, l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	97 // float scarr[26];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	98 float **cpmxpd = floatwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	99 int **cpmxpdn = intwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	100 int count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	101 float *matchpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	102 float **cpmxpdpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	103 int **cpmxpdnpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	104 int cpkd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	105 float *scarr;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	106 scarr = calloc( nalphabets, sizeof( float ) );
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 if( initialize )
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 for( j=0; j<lgth2; j++ )
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 count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	113 for( l=0; l<nalphabets; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	114 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	115 if( cpmx2[j][l] )
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 cpmxpd[j][count] = cpmx2[j][l];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	118 cpmxpdn[j][count] = l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	119 count++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	120 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	121 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	122 cpmxpdn[j][count] = -1;
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 }
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 for( l=0; l<nalphabets; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	127 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	128 scarr[l] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	129 for( k=0; k<nalphabets; k++ )
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 scarr[l] += (n_dis[k][l]-RNAthr) * cpmx1[i1][k];
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 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	134 #if 0 /* ��Ȥ��Ȥ��floatwork�Υ��Ȥ�դˤ�� */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	135 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	136 float fpt, fptpt, fpt2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	137 int ipt, *iptpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	138 fpt2 = match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	139 iptpt = cpmxpdn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	140 fptpt = cpmxpd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	141 while( lgth2-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	142 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	143 *fpt2 = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	144 ipt=iptpt,fpt=fptpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	145 while( *ipt > -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	146 fpt2 += scarr[ipt++] * *fpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	147 fpt2++,iptpt++,fptpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	148 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	149 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	150 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	151 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	152 match[j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	153 for( k=0; cpmxpdn[j][k]>-1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	154 match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	155 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	156 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	157 matchpt = match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	158 cpmxpdnpt = cpmxpdn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	159 cpmxpdpt = cpmxpd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	160 while( lgth2-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	161 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	162 *matchpt = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	163 for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	164 matchpt += scarr[cpkd] (*cpmxpdpt)[k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	165 matchpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	166 cpmxpdnpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	167 cpmxpdpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	168 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	169 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	170 free( scarr );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	171 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	172
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	173 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	174 static void match_add( float match, float cpmx1, float cpmx2, int i1, int lgth2, float floatwork, int *intwork, int initialize )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	175 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	176 int j, k, l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	177 float scarr[nalphabets];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	178 float **cpmxpd = floatwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	179 int **cpmxpdn = intwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	180 int count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	181 float *matchpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	182 float **cpmxpdpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	183 int **cpmxpdnpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	184 int cpkd;
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 if( initialize )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	188 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	189 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	190 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	191 count = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	192 for( l=0; l<nalphabets; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	193 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	194 if( cpmx2[j][l] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	195 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	196 cpmxpd[j][count] = cpmx2[j][l];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	197 cpmxpdn[j][count] = l;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	198 count++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	199 }
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 cpmxpdn[j][count] = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	202 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	203 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	204
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	205 for( l=0; l<nalphabets; l++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	206 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	207 scarr[l] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	208 for( k=0; k<nalphabets; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	209 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	210 scarr[l] += n_dis[k][l] * cpmx1[i1][k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	211 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	212 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	213 #if 0 /* ��Ȥ��Ȥ��floatwork�Υ��Ȥ�դˤ�� */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	214 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	215 float fpt, fptpt, fpt2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	216 int ipt, *iptpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	217 fpt2 = match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	218 iptpt = cpmxpdn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	219 fptpt = cpmxpd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	220 while( lgth2-- )
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 *fpt2 = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	223 ipt=iptpt,fpt=fptpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	224 while( *ipt > -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	225 fpt2 += scarr[ipt++] * *fpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	226 fpt2++,iptpt++,fptpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	227 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	228 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	229 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	230 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	231 match[j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	232 for( k=0; cpmxpdn[j][k]>-1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	233 match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	234 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	235 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	236 matchpt = match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	237 cpmxpdnpt = cpmxpdn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	238 cpmxpdpt = cpmxpd;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	239 while( lgth2-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	240 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	241 // *matchpt = 0.0; // add dakara
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	242 for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	243 matchpt += scarr[cpkd] (*cpmxpdpt)[k];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	244 matchpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	245 cpmxpdnpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	246 cpmxpdpt++;
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	249 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	250 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	251
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	252 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	253 static float Atracking(
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	254 char seq1, char seq2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	255 char mseq1, char mseq2,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	256 int **ijp, int icyc, int jcyc,
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	257 int ist, int ien, int jst, int jen )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	258 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	259 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	260 char gaptable1, gt1bk;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	261 char gaptable2, gt2bk;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	262 lgth1 = ien-ist+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	263 lgth2 = jen-jst+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	264
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	265 gt1bk = AllocateCharVec( lgth1+lgth2+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	266 gt2bk = AllocateCharVec( lgth1+lgth2+1 );
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	269 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	270 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	271 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	272 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	273 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	274
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 // fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	277
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	278 for( i=0; i<lgth1+1; i++ )
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 ijp[i][0] = i + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	281 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	282 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	283 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	284 ijp[0][j] = -( j + 1 );
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	287
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	288 gaptable1 = gt1bk + lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	289 *gaptable1 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	290 gaptable2 = gt2bk + lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	291 *gaptable2 = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	292
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	293 // if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	294
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	295 iin = lgth1; jin = lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	296 klim = lgth1+lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	297 for( k=0; k<=klim; k++ )
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 if( ijp[iin][jin] < 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	300 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	301 ifi = iin-1; jfi = jin+ijp[iin][jin];
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 else if( ijp[iin][jin] > 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	304 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	305 ifi = iin-ijp[iin][jin]; jfi = jin-1;
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 else
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 ifi = iin-1; jfi = jin-1;
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 l = iin - ifi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	312 while( --l )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	313 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	314 *--gaptable1 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	315 *--gaptable2 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	316 k++;
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 l= jin - jfi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	319 while( --l )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	320 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	321 *--gaptable1 = '-';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	322 *--gaptable2 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	323 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	324 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	325 if( iin <= 0 \|\| jin <= 0 ) break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	326 *--gaptable1 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	327 *--gaptable2 = 'o';
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	328 k++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	329 iin = ifi; jin = jfi;
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 for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	334 for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );
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 free( gt1bk );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	337 free( gt2bk );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	338
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	339 // fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	340 // fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	341 return( 0.0 );
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	344
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 static float MSalign2m2m_rec( int icyc, int jcyc, double eff1, double eff2, char seq1, char seq2, float cpmx1, float cpmx2, int ist, int ien, int jst, int jen, int alloclen, char mseq1, char mseq2, int depth, float gapinfo, float map )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	347 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	348 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	349 float value = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	350 register int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	351 char aseq1, aseq2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	352 int ll1, ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	353 int lasti, lastj, imid, jmid = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	354 float wm = 0.0; /* int ?????? */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	355 float g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	356 float currentw, previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	357 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	358 float fpenalty_ex = (float)penalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	359 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	360 // float fpenalty = (float)penalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	361 float *wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	362 // short *ijppt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	363 int *mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	364 // short **ijp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	365 int *mp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	366 int mpi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	367 float mjpt, prept, *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	368 float mi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	369 float *m;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	370 float w1, w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	371 // float *match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	372 float initverticalw; / kufuu sureba iranai */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	373 float lastverticalw; / kufuu sureba iranai */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	374 int **intwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	375 float **floatwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	376 // short **shortmtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	377 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	378 float **WMMTX;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	379 float **WMMTX2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	380 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	381 float *midw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	382 float *midm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	383 float *midn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	384 int lgth1, lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	385 float maxwm = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	386 int *jumpforwi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	387 int *jumpforwj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	388 int *jumpbacki;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	389 int *jumpbackj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	390 int *jumpdummi; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	391 int *jumpdummj; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	392 int jumpi, jumpj = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	393 char *gaps;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	394 int ijpi, ijpj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	395 float *ogcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	396 float *fgcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	397 float *ogcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	398 float *fgcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	399 float firstm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	400 int firstmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	401 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	402 static char ttt1[50000];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	403 static char ttt2[50000];
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 localthr = -offset + 500; // 0?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	407
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	408 ogcp1 = gapinfo[0] + ist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	409 fgcp1 = gapinfo[1] + ist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	410 ogcp2 = gapinfo[2] + jst;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	411 fgcp2 = gapinfo[3] + jst;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	412
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	413 depth++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	414 reccycle++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	415
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	416 lgth1 = ien-ist+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	417 lgth2 = jen-jst+1;
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( lgth1 < 5 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	420 // fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	421 // if( lgth2 < 5 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	422 // fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	423 //
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	426 fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	427 strncpy( ttt1, seq1[0]+ist, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	428 strncpy( ttt2, seq2[0]+jst, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	429 ttt1[lgth1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	430 ttt2[lgth2] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	431 fprintf( stderr, "seq1 = %s\n", ttt1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	432 fprintf( stderr, "seq2 = %s\n", ttt2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	433 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	434 if( lgth2 <= 0 ) // lgth1 <= 0 ha?
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 // fprintf( stderr, "\n\n==== jimei\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	437 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	438 for( i=0; i<icyc; 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( mseq1[i], seq1[i]+ist, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	441 mseq1[i][lgth1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	442 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	443 for( i=0; i<jcyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	444 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	445 mseq2[i][0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	446 for( j=0; j<lgth1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	447 strcat( mseq2[i], "-" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	448 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	449
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	450 // fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	451 // fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	452
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	453 return( 0.0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	454 }
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 #if MEMSAVE
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	457 aseq1 = AllocateCharMtx( icyc, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	458 aseq2 = AllocateCharMtx( jcyc, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	459 for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	460 for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	461 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	462 aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	463 aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	464 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	465
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	466 // if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	467 // if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	468 if( lgth1 < DPTANNI \|\| lgth2 < DPTANNI ) // zettai ni anzen ka?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	469 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	470 // fprintf( stderr, "==== Going to _tanni\n" );
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 // value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
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 #if MEMSAVE
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	476 free( aseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	477 free( aseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	478 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	479 for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	480 for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	481
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	482 FreeCharMtx( aseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	483 FreeCharMtx( aseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	484 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	485
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	486 // fprintf( stderr, "value = %f\n", value );
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 return( value );
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 // fprintf( stderr, "Trying to divide the mtx\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	491
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	492 ll1 = ( (int)(lgth1) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	493 ll2 = ( (int)(lgth2) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	494
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	495 // fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	496
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	497 w1 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	498 w2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	499 // match = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	500 midw = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	501 midn = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	502 midm = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	503 jumpbacki = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	504 jumpbackj = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	505 jumpforwi = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	506 jumpforwj = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	507 jumpdummi = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	508 jumpdummj = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	509
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	510 initverticalw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	511 lastverticalw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	512
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	513 m = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	514 mp = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	515 gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	516
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	517 floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	518 intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets );
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 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	521 fprintf( stderr, "succeeded\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	522 #endif
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 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	525 WMMTX = AllocateFloatMtx( ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	526 WMMTX2 = AllocateFloatMtx( ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	527 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	528 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	529 shortmtx = AllocateShortMtx( ll1, ll2 );
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 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	532 fprintf( stderr, "succeeded\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	533 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	534
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	535 ijp = shortmtx;
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 currentw = w1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	539 previousw = w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	540
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	541 match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	542
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	543 match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
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 for( i=1; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	546 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	547 initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
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 for( j=1; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	550 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	551 currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	552 }
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 STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	555 WMMTX[0][0] = initverticalw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	556 for( i=1; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	557 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	558 WMMTX[i][0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	559 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	560 for( j=1; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	561 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	562 WMMTX[0][j] = currentw[j];
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 #endif
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	567 for( j=1; j<lgth2+1; ++j )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	568 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	569 m[j] = currentw[j-1] + ogcp1[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	570 // m[j] = currentw[j-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	571 mp[j] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	572 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	573
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	574 lastverticalw[0] = currentw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	575
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	576 imid = lgth1 * 0.5;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	577
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	578 jumpi = 0; // atode kawaru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	579 lasti = lgth1+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	580 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	581 for( i=1; i<lasti; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	582 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	583 for( i=1; i<=imid; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	584 #endif
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 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	587 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	588 currentw = wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	589
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	590 previousw[0] = initverticalw[i-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	591
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	592 match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	593 currentw[0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	594
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	595 m[0] = ogcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	596 #if STOREM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	597 WMMTX2[i][0] = m[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	598 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	599 if( i == imid ) midm[0] = m[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	600
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	601 mi = previousw[0] + ogcp2[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	602 // mi = previousw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	603 mpi = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	604
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	605
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	606 // ijppt = ijp[i] + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	607 mjpt = m + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	608 prept = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	609 curpt = currentw + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	610 mpjpt = mp + 1;
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 lastj = lgth2+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	614 for( j=1; j<lastj; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	615 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	616
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	617 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	618
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	619 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	620 fprintf( stderr, "%5.0f->", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	621 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	622 g = mi + fgcp2[j-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	623 // g = mi + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	624 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	625 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	626 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	627 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	628 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	629 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	630 // *ijppt = -( j - mpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	631 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	632 g = *prept + ogcp2[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	633 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	634 if( g >= mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	635 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	636 mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	637 mpi = j-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	638 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	639 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	640 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	641 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	642
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	643 g = *mjpt + fgcp1[i-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	644 // g = *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	645 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	646 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	647 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	648 if( g > wm )
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 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	651 // ijppt = +( i - mpjpt );
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	654
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	655 g = *prept + ogcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	656 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	657 if( g >= *mjpt )
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 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	660 *mpjpt = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	661 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	662 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	663 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	664 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	665 #if LOCAL
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	666 if( wm < localthr )
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 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	669 wm = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	670 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	671 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	672
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	673 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	674 fprintf( stderr, "%5.0f ", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	675 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	676 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	677
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 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	680 WMMTX[i][j] = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	681 WMMTX2[i][j] = *mjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	682 #endif
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 if( i == imid ) //muda
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 jumpbackj[j] = *mpjpt; // muda atode matomeru
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	687 jumpbacki[j] = mpi; // muda atode matomeru
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	688 // fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	689 // fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	690 midw[j] = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	691 midm[j] = *mjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	692 midn[j] = mi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	693 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	694
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	695 // fprintf( stderr, "m[%d] = %f\n", j, m[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	696 mjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	697 prept++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	698 mpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	699 curpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	700
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 lastverticalw[i] = currentw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	703
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	704 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	705 WMMTX2[i][lgth2] = m[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	706 #endif
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 #if 0 // ue
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	709 if( i == imid )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	710 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	711 for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	712 for( j=0; j<lgth2; j++ ) midm[j] = m[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	713 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	714 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	715 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	716 // for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	717 // for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	718
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	719 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	720 for( i=0; i<lgth1; i++ )
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 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	723 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	724 fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
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 fprintf( stderr, "\n" );
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, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	729 fprintf( stderr, "WMMTX2 = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	730 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	731 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	732 for( j=0; j<lgth2; j++ )
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 fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
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, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	737 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	738 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	739 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	740
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	741 // gyakudp
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 match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	744 match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	745
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	746 for( i=0; i<lgth1-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	747 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	748 initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	749 // initverticalw[i] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	750 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	751 for( j=0; j<lgth2-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	752 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	753 currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	754 // currentw[j] += fpenalty;
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	757 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	758 for( i=0; i<lgth1-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	759 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	760 WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	761 // fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
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 for( j=0; j<lgth2-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	764 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	765 WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	766 // fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
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 #endif
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
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
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	775 for( j=lgth2-1; j>0; --j )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	776 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	777 m[j-1] = currentw[j] + fgcp2[lgth2-2];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	778 // m[j-1] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	779 mp[j] = lgth1-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	780 }
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 // for( j=0; j<lgth2; j++ ) m[j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	783 // m[lgth2-1] ha irunoka?
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 // for( i=lgth1-2; i>=imid; i-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	787 firstm = -9999999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	788 firstmp = lgth1-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	789 for( i=lgth1-2; i>-1; i-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	790 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	791 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	792 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	793 currentw = wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	794 previousw[lgth2-1] = initverticalw[i+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	795 // match_calc( currentw, seq1, seq2, i, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	796 match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	797
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	798 currentw[lgth2-1] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	799
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	800 // m[lgth2] = fgcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	801 // WMMTX2[i][lgth2] += m[lgth2];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	802 // fprintf( stderr, "m[] = %f\n", m[lgth2] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	803
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	804 mi = previousw[lgth2-1] + fgcp2[lgth2-2];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	805 // mi = previousw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	806 mpi = lgth2 - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	807
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	808 mjpt = m + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	809 prept = previousw + lgth2 - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	810 curpt = currentw + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	811 mpjpt = mp + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	812
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	813
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	814 for( j=lgth2-2; j>-1; j-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	815 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	816 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	817 ijpi = i+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	818 ijpj = j+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	819
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	820 g = mi + ogcp2[j+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	821 // g = mi + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	822 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	823 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	824 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	825 ijpj = mpi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	826 ijpi = i+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	827 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	828
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	829 g = *prept + fgcp2[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	830 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	831 if( g >= mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	832 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	833 // fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	834 mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	835 mpi = j + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	836 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	837
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	838 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	839 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	840 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	841
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	842 // fprintf( stderr, "i,j=%d,%d mpjpt = %d\n", i, j, mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	843 g = *mjpt + ogcp1[i+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	844 // g = *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	845 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	846 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	847 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	848 ijpi = *mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	849 ijpj = j+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	850 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	851
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	852 // if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	853 g = *prept + fgcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	854 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	855 if( g >= *mjpt )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	856 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	857 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	858 *mpjpt = i + 1;
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	861 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	862 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	863 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	864
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	865 if( i == jumpi \|\| i == imid - 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	866 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	867 jumpforwi[j] = ijpi; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	868 jumpforwj[j] = ijpj; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	869 // fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	870 // fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	871 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	872 if( i == imid ) // muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	873 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	874 midw[j] += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	875 // midm[j+1] += *mjpt + fpenalty; //??????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	876 midm[j+1] += *mjpt; //??????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	877 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	878 if( i == imid - 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	879 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	880 // midn[j] += mi + fpenalty; //????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	881 midn[j] += mi; //????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	882 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	883 #if LOCAL
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	884 if( wm < localthr )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	885 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	886 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	887 wm = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	888 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	889 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	890
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	891 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	892 WMMTX[i][j] += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	893 // WMMTX2[i][j+1] += *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	894 WMMTX2[i][j] += *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	895 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	896 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	897
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	898 mjpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	899 prept--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	900 mpjpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	901 curpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	902 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	903 // fprintf( stderr, "adding mjpt (=%f) to WMMTX2[%d][%d]\n", mjpt, i, j+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	904 g = *prept + fgcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	905 if( firstm < g )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	906 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	907 firstm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	908 firstmp = i + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	909 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	910 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	911 // WMMTX2[i][j+1] += firstm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	912 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	913 if( i == imid ) midm[j+1] += firstm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	914
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	915 if( i == imid - 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	916 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	917 maxwm = midw[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	918 jmid = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	919 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	920 for( j=2; j<lgth2-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	921 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	922 wm = midw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	923 if( wm > maxwm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	924 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	925 jmid = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	926 maxwm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	927 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	928 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	929 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	930 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	931 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	932 wm = midm[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	933 if( wm > maxwm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	934 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	935 jmid = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	936 maxwm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	937 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	938 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	939 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	940
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	941 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	942
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	943
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	944 // fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	945 wm = midw[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	946 jumpi = imid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	947 jumpj = jmid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	948 if( jmid > 0 && midn[jmid-1] > wm ) //060413
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	949 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	950 jumpi = imid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	951 jumpj = jumpbacki[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	952 wm = midn[jmid-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	953 // fprintf( stderr, "rejump (n)\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	954 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	955 if( midm[jmid] > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	956 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	957 jumpi = jumpbackj[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	958 jumpj = jmid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	959 wm = midm[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	960 // fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	961 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	962
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	963
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	964 // fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	965 // fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	966 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	967 fprintf( stderr, "imid = %d\n", imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	968 fprintf( stderr, "midn = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	969 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	970 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	971 fprintf( stderr, "% 7.1f ", midn[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	972 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	973 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	974 fprintf( stderr, "midw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	975 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	976 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	977 fprintf( stderr, "% 7.1f ", midw[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	978 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	979 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	980 fprintf( stderr, "midm = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	981 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	982 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	983 fprintf( stderr, "% 7.1f ", midm[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	984 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	985 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	986 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	987 // fprintf( stderr, "maxwm = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	988 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	989 if( i == jumpi ) //saki?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	990 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	991 // fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	992 // fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	993 if( jmid == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	994 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	995 // fprintf( stderr, "CHUI2!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	996 jumpj = 0; jmid = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	997 jumpi = firstmp - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	998 imid = firstmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	999 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1000
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1001 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1002 else if( jmid == lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1003 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1004 fprintf( stderr, "CHUI1!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1005 jumpi=0; jumpj=0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1006 imid=jumpforwi[0]; jmid=lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1007 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1008 #else // 060414
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1009 else if( jmid >= lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1010 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1011 // fprintf( stderr, "CHUI1!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1012 jumpi=imid-1; jmid=lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1013 jumpj = lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1014 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1015 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1016 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1017 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1018 imid = jumpforwi[jumpj];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1019 jmid = jumpforwj[jumpj];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1020 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1021 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1022 fprintf( stderr, "jumpi -> %d\n", jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1023 fprintf( stderr, "jumpj -> %d\n", jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1024 fprintf( stderr, "imid -> %d\n", imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1025 fprintf( stderr, "jmid -> %d\n", jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1026 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1027
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1028 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1029 // break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1030 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1031 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1032 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1033 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1034 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1035 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1036 jumpi=0; jumpj=0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1037 imid=lgth1-1; jmid=lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1038 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1039 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1040
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1041 // fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1042 // fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1043
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1044 // for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1045 // for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1046 // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1047 // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1048
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1049
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1050
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1051 for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1052 map[i][j] = WMMTX[i][j] / maxwm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1053 // map[i][j] = WMMTX2[i][j] / maxwm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1054
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1055 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1056
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1057 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1058 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1059 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1060 float maxpairscore = -9999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1061 float tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1062
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1063 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1064 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1065 if( maxpairscore < (tmpscore=WMMTX[i][j]) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1066 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1067 map12[i].pos = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1068 map12[i].score = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1069 maxpairscore = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1070 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1071 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1072
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1073 for( k=0; k<lgth1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1074 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1075 if( i == k ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1076 if( map12[i].score <= WMMTX[k][map12[i].pos] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1077 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1078 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1079 if( k != lgth1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1080 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1081 map12[i].pos = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1082 map12[i].score = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1083 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1084 fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1085 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1086 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1087 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1088 float maxpairscore = -9999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1089 float tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1090
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1091 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1092 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1093 if( maxpairscore < (tmpscore=WMMTX[i][j]) )
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 map21[j].pos = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1096 map21[j].score = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1097 maxpairscore = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1098 }
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1101 for( k=0; k<lgth2; k++ )
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( j == k ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1104 if( map21[j].score <= WMMTX[map21[j].pos][k] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1105 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1106 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1107 if( k != lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1108 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1109 map21[j].pos = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1110 map21[j].score = -1.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1111 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1112 fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1113 }
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 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1116 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1117 if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1118 fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1121
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1122 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1123 fprintf( stderr, "WMMTX = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1124 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1125 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1126 fprintf( stderr, "%d ", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1127 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1128 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1129 fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1130 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1131 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1132 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1133 // fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1134 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1135 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1136 fprintf( stderr, "%d ", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1137 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1138 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1139 fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1140 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1141 fprintf( stderr, "\n" );
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 #endif
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1146 fprintf( stdout, "#WMMTX = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1147 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1148 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1149 // fprintf( stdout, "%d ", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1150 for( j=0; j<lgth2; j++ )
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 // if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1153 fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1154 if( WMMTX[i][j] == maxwm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1155 fprintf( stdout, "selected \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1156 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1157 fprintf( stdout, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1158 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1159 fprintf( stdout, "\n" );
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1162
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1163 #if 0
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 fprintf( stderr, "jumpbacki = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1166 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1167 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1168 fprintf( stderr, "% 7d ", jumpbacki[j] );
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 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1171 fprintf( stderr, "jumpbackj = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1172 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1173 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1174 fprintf( stderr, "% 7d ", jumpbackj[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1175 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1176 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1177 fprintf( stderr, "jumpforwi = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1178 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1179 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1180 fprintf( stderr, "% 7d ", jumpforwi[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1181 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1182 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1183 fprintf( stderr, "jumpforwj = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1184 for( j=0; j<lgth2; j++ )
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 fprintf( stderr, "% 7d ", jumpforwj[j] );
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 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1189 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1190
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1191
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1192 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1193
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1194
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1195 // Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
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 #if 0 // irukamo
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1198 resultlen = strlen( mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1199 if( alloclen < resultlen \|\| resultlen > N )
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 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1202 ErrorExit( "LENGTH OVER!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1203 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1204 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1205
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1206
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1207
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1208 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1209 fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1210 fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
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 fprintf( stderr, "imid = %d\n", imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1213 fprintf( stderr, "jmid = %d\n", jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1214 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1215
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1216
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1217 FreeFloatVec( w1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1218 FreeFloatVec( w2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1219 FreeFloatVec( initverticalw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1220 FreeFloatVec( lastverticalw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1221 FreeFloatVec( midw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1222 FreeFloatVec( midm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1223 FreeFloatVec( midn );
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 FreeIntVec( jumpbacki );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1226 FreeIntVec( jumpbackj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1227 FreeIntVec( jumpforwi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1228 FreeIntVec( jumpforwj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1229 FreeIntVec( jumpdummi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1230 FreeIntVec( jumpdummj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1231
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1232 FreeFloatVec( m );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1233 FreeIntVec( mp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1234
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1235 FreeFloatMtx( floatwork );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1236 FreeIntMtx( intwork );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1237
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1238 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1239 FreeFloatMtx( WMMTX );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1240 FreeFloatMtx( WMMTX2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1241 #endif
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 return( value );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1244
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 static float MSalignmm_rec( int icyc, int jcyc, double eff1, double eff2, char seq1, char seq2, float cpmx1, float cpmx2, int ist, int ien, int jst, int jen, int alloclen, char mseq1, char mseq2, int depth, float gapinfo, float map )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1247 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1248 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1249 float value = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1250 register int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1251 char aseq1, aseq2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1252 int ll1, ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1253 int lasti, lastj, imid, jmid=0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1254 float wm = 0.0; /* int ?????? */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1255 float g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1256 float currentw, previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1257 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1258 float fpenalty_ex = (float)RNApenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1259 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1260 // float fpenalty = (float)penalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1261 float *wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1262 // short *ijppt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1263 int *mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1264 // short **ijp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1265 int *mp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1266 int mpi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1267 float mjpt, prept, *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1268 float mi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1269 float *m;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1270 float w1, w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1271 // float *match;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1272 float initverticalw; / kufuu sureba iranai */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1273 float lastverticalw; / kufuu sureba iranai */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1274 int **intwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1275 float **floatwork;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1276 // short **shortmtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1277 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1278 float **WMMTX;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1279 float **WMMTX2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1280 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1281 float *midw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1282 float *midm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1283 float *midn;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1284 int lgth1, lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1285 float maxwm = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1286 int *jumpforwi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1287 int *jumpforwj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1288 int *jumpbacki;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1289 int *jumpbackj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1290 int *jumpdummi; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1291 int *jumpdummj; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1292 int jumpi, jumpj = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1293 char *gaps;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1294 int ijpi, ijpj;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1295 float *ogcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1296 float *fgcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1297 float *ogcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1298 float *fgcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1299 float firstm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1300 int firstmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1301 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1302 static char ttt1[50000];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1303 static char ttt2[50000];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1304 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1305
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1306 localthr = -offset + 500; // 0?
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 ogcp1 = gapinfo[0] + ist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1309 fgcp1 = gapinfo[1] + ist;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1310 ogcp2 = gapinfo[2] + jst;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1311 fgcp2 = gapinfo[3] + jst;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1312
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1313 depth++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1314 reccycle++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1315
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1316 lgth1 = ien-ist+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1317 lgth2 = jen-jst+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1318
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1319 // if( lgth1 < 5 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1320 // fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1321 // if( lgth2 < 5 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1322 // fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1326 fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1327 strncpy( ttt1, seq1[0]+ist, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1328 strncpy( ttt2, seq2[0]+jst, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1329 ttt1[lgth1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1330 ttt2[lgth2] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1331 fprintf( stderr, "seq1 = %s\n", ttt1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1332 fprintf( stderr, "seq2 = %s\n", ttt2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1333 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1334 if( lgth2 <= 0 ) // lgth1 <= 0 ha?
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 // fprintf( stderr, "\n\n==== jimei\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1337 // exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1338 for( i=0; i<icyc; i++ )
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 strncpy( mseq1[i], seq1[i]+ist, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1341 mseq1[i][lgth1] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1342 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1343 for( i=0; i<jcyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1344 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1345 mseq2[i][0] = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1346 for( j=0; j<lgth1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1347 strcat( mseq2[i], "-" );
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1350 // fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1351 // fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1352
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1353 return( 0.0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1354 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1355
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1356 #if MEMSAVE
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1357 aseq1 = AllocateCharMtx( icyc, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1358 aseq2 = AllocateCharMtx( jcyc, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1359 for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1360 for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1361 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1362 aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1363 aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1364 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1365
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1366 // if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1367 // if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1368 if( lgth1 < DPTANNI \|\| lgth2 < DPTANNI ) // zettai ni anzen ka?
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1369 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1370 // fprintf( stderr, "==== Going to _tanni\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1371
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1372 // value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );
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 #if MEMSAVE
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1376 free( aseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1377 free( aseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1378 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1379 for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1380 for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1381
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1382 FreeCharMtx( aseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1383 FreeCharMtx( aseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1384 #endif
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 // fprintf( stderr, "value = %f\n", value );
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 return( value );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1389 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1390 // fprintf( stderr, "Trying to divide the mtx\n" );
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 ll1 = ( (int)(lgth1) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1393 ll2 = ( (int)(lgth2) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1394
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1395 // fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1396
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1397 w1 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1398 w2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1399 // match = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1400 midw = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1401 midn = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1402 midm = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1403 jumpbacki = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1404 jumpbackj = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1405 jumpforwi = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1406 jumpforwj = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1407 jumpdummi = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1408 jumpdummj = AllocateIntVec( ll2+2 );
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 initverticalw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1411 lastverticalw = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1412
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1413 m = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1414 mp = AllocateIntVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1415 gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1416
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1417 floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1418 intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1419
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1420 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1421 fprintf( stderr, "succeeded\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1422 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1423
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1424 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1425 WMMTX = AllocateFloatMtx( ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1426 WMMTX2 = AllocateFloatMtx( ll1, ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1427 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1428 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1429 shortmtx = AllocateShortMtx( ll1, ll2 );
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 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1432 fprintf( stderr, "succeeded\n\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1433 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1434
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1435 ijp = shortmtx;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1436 #endif
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 currentw = w1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1439 previousw = w2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1440
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1441 match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1442
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1443 match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1444
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1445 for( i=1; i<lgth1+1; i++ )
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 initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1448 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1449 for( j=1; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1450 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1451 currentw[j] += ( ogcp2[0] + fgcp2[j-1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1452 }
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 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1455 WMMTX[0][0] = initverticalw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1456 for( i=1; i<lgth1+1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1457 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1458 WMMTX[i][0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1459 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1460 for( j=1; j<lgth2+1; j++ )
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 WMMTX[0][j] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1463 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1464 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1465
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1466
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1467 for( j=1; j<lgth2+1; ++j )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1468 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1469 m[j] = currentw[j-1] + ogcp1[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1470 // m[j] = currentw[j-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1471 mp[j] = 0;
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1474 lastverticalw[0] = currentw[lgth2-1];
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 imid = lgth1 * 0.5;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1477
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1478 jumpi = 0; // atode kawaru.
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1479 lasti = lgth1+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1480 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1481 for( i=1; i<lasti; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1482 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1483 for( i=1; i<=imid; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1484 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1485 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1486 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1487 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1488 currentw = wtmp;
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 previousw[0] = initverticalw[i-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1491
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1492 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1493 currentw[0] = initverticalw[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1494
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1495 m[0] = ogcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1496 #if STOREM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1497 WMMTX2[i][0] = m[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1498 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1499 if( i == imid ) midm[0] = m[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1500
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1501 mi = previousw[0] + ogcp2[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1502 // mi = previousw[0];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1503 mpi = 0;
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1506 // ijppt = ijp[i] + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1507 mjpt = m + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1508 prept = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1509 curpt = currentw + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1510 mpjpt = mp + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1511
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1512
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1513 lastj = lgth2+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1514 for( j=1; j<lastj; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1515 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1516
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1517 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1518
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1519 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1520 fprintf( stderr, "%5.0f->", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1521 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1522 g = mi + fgcp2[j-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1523 // g = mi + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1524 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1525 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1526 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1527 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1528 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1529 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1530 // *ijppt = -( j - mpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1531 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1532 g = *prept + ogcp2[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1533 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1534 if( g >= mi )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1535 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1536 mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1537 mpi = j-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1538 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1539 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1540 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1541 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1542
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1543 g = *mjpt + fgcp1[i-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1544 // g = *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1545 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1546 fprintf( stderr, "%5.0f?", g );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1547 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1548 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1549 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1550 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1551 // ijppt = +( i - mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1552 }
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 g = *prept + ogcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1556 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1557 if( g >= *mjpt )
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 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1560 *mpjpt = i-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1561 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1562 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1563 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1564 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1565 #if LOCAL
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1566 if( wm < localthr )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1567 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1568 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1569 wm = 0;
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 #endif
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1574 fprintf( stderr, "%5.0f ", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1575 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1576 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1577
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 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1580 WMMTX[i][j] = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1581 WMMTX2[i][j] = *mjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1582 #endif
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 if( i == imid ) //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1585 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1586 jumpbackj[j] = *mpjpt; // muda atode matomeru
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1587 jumpbacki[j] = mpi; // muda atode matomeru
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1588 // fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1589 // fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1590 midw[j] = *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1591 midm[j] = *mjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1592 midn[j] = mi;
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1595 // fprintf( stderr, "m[%d] = %f\n", j, m[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1596 mjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1597 prept++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1598 mpjpt++;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1599 curpt++;
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 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1602 lastverticalw[i] = currentw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1603
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1604 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1605 WMMTX2[i][lgth2] = m[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1606 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1607
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1608 #if 0 // ue
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1609 if( i == imid )
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 for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1612 for( j=0; j<lgth2; j++ ) midm[j] = m[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1613 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1614 #endif
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 // for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1617 // for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1618
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1619 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1620 for( i=0; i<lgth1; i++ )
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( j=0; j<lgth2; j++ )
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 fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1625 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1626 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1627 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1628 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1629 fprintf( stderr, "WMMTX2 = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1630 for( i=0; i<lgth1; i++ )
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 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1633 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1634 fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1635 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1636 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1637 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1638 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1639 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1640
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1641 // gyakudp
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1642
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1643 match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1644 match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
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 for( i=0; i<lgth1-1; i++ )
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 initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1649 // initverticalw[i] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1650 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1651 for( j=0; j<lgth2-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1652 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1653 currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1654 // currentw[j] += fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1655 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1656
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1657 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1658 for( i=0; i<lgth1-1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1659 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1660 WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1661 // fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1662 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1663 for( j=0; j<lgth2-1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1664 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1665 WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1666 // fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1667 }
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1671
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1672
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1673
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 for( j=lgth2-1; j>0; --j )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1676 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1677 m[j-1] = currentw[j] + fgcp2[lgth2-2];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1678 // m[j-1] = currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1679 mp[j] = lgth1-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1680 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1681
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1682 // for( j=0; j<lgth2; j++ ) m[j] = 0.0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1683 // m[lgth2-1] ha irunoka?
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1686 // for( i=lgth1-2; i>=imid; i-- )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1687 firstm = -9999999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1688 firstmp = lgth1-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1689 for( i=lgth1-2; i>-1; i-- )
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 wtmp = previousw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1692 previousw = currentw;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1693 currentw = wtmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1694 previousw[lgth2-1] = initverticalw[i+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1695 // match_calc( currentw, seq1, seq2, i, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1696 match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1697
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1698 currentw[lgth2-1] = initverticalw[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 // m[lgth2] = fgcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1701 // WMMTX2[i][lgth2] += m[lgth2];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1702 // fprintf( stderr, "m[] = %f\n", m[lgth2] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1703
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1704 mi = previousw[lgth2-1] + fgcp2[lgth2-2];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1705 // mi = previousw[lgth2-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1706 mpi = lgth2 - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1707
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1708 mjpt = m + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1709 prept = previousw + lgth2 - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1710 curpt = currentw + lgth2 - 2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1711 mpjpt = mp + lgth2 - 2;
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1714 for( j=lgth2-2; j>-1; j-- )
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 wm = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1717 ijpi = i+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1718 ijpj = j+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1719
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1720 g = mi + ogcp2[j+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1721 // g = mi + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1722 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1723 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1724 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1725 ijpj = mpi;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1726 ijpi = i+1;
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 g = *prept + fgcp2[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1730 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1731 if( g >= mi )
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 // fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1734 mi = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1735 mpi = j + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1736 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1737
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1738 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1739 mi += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1740 #endif
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 // fprintf( stderr, "i,j=%d,%d mpjpt = %d\n", i, j, mpjpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1743 g = *mjpt + ogcp1[i+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1744 // g = *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1745 if( g > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1746 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1747 wm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1748 ijpi = *mpjpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1749 ijpj = j+1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1750 }
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 // if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1753 g = *prept + fgcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1754 // g = *prept;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1755 if( g >= *mjpt )
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 *mjpt = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1758 *mpjpt = i + 1;
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 #if USE_PENALTY_EX
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1762 m[j] += fpenalty_ex;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1763 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1764
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1765 if( i == jumpi \|\| i == imid - 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1766 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1767 jumpforwi[j] = ijpi; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1768 jumpforwj[j] = ijpj; //muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1769 // fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1770 // fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1771 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1772 if( i == imid ) // muda
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1773 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1774 midw[j] += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1775 // midm[j+1] += *mjpt + fpenalty; //??????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1776 midm[j+1] += *mjpt; //??????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1777 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1778 if( i == imid - 1 )
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 // midn[j] += mi + fpenalty; //????
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1781 midn[j] += mi; //????
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 #if LOCAL
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1784 if( wm < localthr )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1785 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1786 // fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1787 wm = 0;
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1790
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1791 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1792 WMMTX[i][j] += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1793 // WMMTX2[i][j+1] += *mjpt + fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1794 WMMTX2[i][j] += *curpt;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1795 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1796 *curpt += wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1797
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1798 mjpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1799 prept--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1800 mpjpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1801 curpt--;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1802 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1803 // fprintf( stderr, "adding mjpt (=%f) to WMMTX2[%d][%d]\n", mjpt, i, j+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1804 g = *prept + fgcp1[i];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1805 if( firstm < g )
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 firstm = g;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1808 firstmp = i + 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1809 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1810 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1811 // WMMTX2[i][j+1] += firstm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1812 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1813 if( i == imid ) midm[j+1] += firstm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1814
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1815 if( i == imid - 1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1816 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1817 maxwm = midw[1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1818 jmid = 0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1819 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1820 for( j=2; j<lgth2-1; j++ )
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 wm = midw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1823 if( wm > maxwm )
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 jmid = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1826 maxwm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1827 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1828 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1829 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1830 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1831 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1832 wm = midm[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1833 if( wm > maxwm )
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 jmid = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1836 maxwm = wm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1837 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1838 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1839 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1840
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1841 // if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1844 // fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1845 wm = midw[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1846 jumpi = imid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1847 jumpj = jmid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1848 if( jmid > 0 && midn[jmid-1] > wm ) //060413
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1849 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1850 jumpi = imid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1851 jumpj = jumpbacki[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1852 wm = midn[jmid-1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1853 // fprintf( stderr, "rejump (n)\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1854 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1855 if( midm[jmid] > wm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1856 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1857 jumpi = jumpbackj[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1858 jumpj = jmid-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1859 wm = midm[jmid];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1860 // fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1861 }
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 // fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1865 // fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1866 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1867 fprintf( stderr, "imid = %d\n", imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1868 fprintf( stderr, "midn = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1869 for( j=0; j<lgth2; j++ )
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 fprintf( stderr, "% 7.1f ", midn[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1872 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1873 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1874 fprintf( stderr, "midw = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1875 for( j=0; j<lgth2; j++ )
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, "% 7.1f ", midw[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1878 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1879 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1880 fprintf( stderr, "midm = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1881 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1882 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1883 fprintf( stderr, "% 7.1f ", midm[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1884 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1885 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1886 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1887 // fprintf( stderr, "maxwm = %f\n", maxwm );
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 if( i == jumpi ) //saki?
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 // fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1892 // fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1893 if( jmid == 0 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1894 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1895 // fprintf( stderr, "CHUI2!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1896 jumpj = 0; jmid = 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1897 jumpi = firstmp - 1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1898 imid = firstmp;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1899 }
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 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1902 else if( jmid == lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1903 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1904 fprintf( stderr, "CHUI1!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1905 jumpi=0; jumpj=0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1906 imid=jumpforwi[0]; jmid=lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1907 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1908 #else // 060414
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1909 else if( jmid >= lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1910 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1911 // fprintf( stderr, "CHUI1!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1912 jumpi=imid-1; jmid=lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1913 jumpj = lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1914 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1915 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1916 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1917 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1918 imid = jumpforwi[jumpj];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1919 jmid = jumpforwj[jumpj];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1920 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1921 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1922 fprintf( stderr, "jumpi -> %d\n", jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1923 fprintf( stderr, "jumpj -> %d\n", jumpj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1924 fprintf( stderr, "imid -> %d\n", imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1925 fprintf( stderr, "jmid -> %d\n", jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1926 #endif
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 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1929 // break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1930 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1931 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1932 #endif
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 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1935 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1936 jumpi=0; jumpj=0;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1937 imid=lgth1-1; jmid=lgth2-1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1938 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1939 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1940
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1941 // fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1942 // fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
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 // for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1945 // for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1946 // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1947 // for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1948
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1949
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 for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1952 map[i][j] = WMMTX[i][j] / maxwm;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1953 // map[i][j] = WMMTX2[i][j] / maxwm;
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 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1956
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1957 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1958 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1959 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1960 float maxpairscore = -9999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1961 float tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1962
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1963 for( j=0; j<lgth2; j++ )
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 if( maxpairscore < (tmpscore=WMMTX[i][j]) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1966 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1967 map12[i].pos = j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1968 map12[i].score = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1969 maxpairscore = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1970 }
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 for( k=0; k<lgth1; k++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1974 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1975 if( i == k ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1976 if( map12[i].score <= WMMTX[k][map12[i].pos] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1977 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1978 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1979 if( k != lgth1 )
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 map12[i].pos = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1982 map12[i].score = -1.0;
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 fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1985 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1986 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1987 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1988 float maxpairscore = -9999.9;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1989 float tmpscore;
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 for( i=0; i<lgth1; i++ )
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( maxpairscore < (tmpscore=WMMTX[i][j]) )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1994 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1995 map21[j].pos = i;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1996 map21[j].score = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1997 maxpairscore = tmpscore;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1998 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	1999 }
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 for( k=0; k<lgth2; k++ )
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 if( j == k ) continue;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2004 if( map21[j].score <= WMMTX[map21[j].pos][k] )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2005 break;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2006 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2007 if( k != lgth2 )
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 map21[j].pos = -1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2010 map21[j].score = -1.0;
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 fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2013 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2014
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2015 for( i=0; i<lgth1; i++ )
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 if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2018 fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2019 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2020 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2021
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2022 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2023 fprintf( stderr, "WMMTX = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2024 for( i=0; i<lgth1; i++ )
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 fprintf( stderr, "%d ", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2027 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2028 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2029 fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
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 fprintf( stderr, "\n" );
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 // fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2034 for( i=0; i<lgth1; i++ )
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 fprintf( stderr, "%d ", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2037 for( j=0; j<lgth2+1; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2038 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2039 fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2040 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2041 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2042 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2043 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2044 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2045
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2046 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2047 fprintf( stdout, "#WMMTX = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2048 for( i=0; i<lgth1; i++ )
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 // fprintf( stdout, "%d ", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2051 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2052 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2053 // if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2054 fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2055 if( WMMTX[i][j] == maxwm )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2056 fprintf( stdout, "selected \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2057 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2058 fprintf( stdout, "\n" );
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 fprintf( stdout, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2061 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2062 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2063 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2064
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2065 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2066
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2067 fprintf( stderr, "jumpbacki = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2068 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2069 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2070 fprintf( stderr, "% 7d ", jumpbacki[j] );
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 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2073 fprintf( stderr, "jumpbackj = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2074 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2075 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2076 fprintf( stderr, "% 7d ", jumpbackj[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2077 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2078 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2079 fprintf( stderr, "jumpforwi = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2080 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2081 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2082 fprintf( stderr, "% 7d ", jumpforwi[j] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2083 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2084 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2085 fprintf( stderr, "jumpforwj = \n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2086 for( j=0; j<lgth2; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2087 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2088 fprintf( stderr, "% 7d ", jumpforwj[j] );
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 fprintf( stderr, "\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2091 #endif
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2094 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2095
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2096
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2097 // Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2098
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2099 #if 0 // irukamo
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2100 resultlen = strlen( mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2101 if( alloclen < resultlen \|\| resultlen > N )
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 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2104 ErrorExit( "LENGTH OVER!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2105 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2106 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2107
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2108
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2109
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2110 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2111 fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2112 fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2113
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2114 fprintf( stderr, "imid = %d\n", imid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2115 fprintf( stderr, "jmid = %d\n", jmid );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2116 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2117
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2118
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2119 FreeFloatVec( w1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2120 FreeFloatVec( w2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2121 FreeFloatVec( initverticalw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2122 FreeFloatVec( lastverticalw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2123 FreeFloatVec( midw );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2124 FreeFloatVec( midm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2125 FreeFloatVec( midn );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2126
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2127 FreeIntVec( jumpbacki );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2128 FreeIntVec( jumpbackj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2129 FreeIntVec( jumpforwi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2130 FreeIntVec( jumpforwj );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2131 FreeIntVec( jumpdummi );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2132 FreeIntVec( jumpdummj );
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 FreeFloatVec( m );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2135 FreeIntVec( mp );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2136
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2137 FreeFloatMtx( floatwork );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2138 FreeIntMtx( intwork );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2139
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2140 #if STOREWM
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2141 FreeFloatMtx( WMMTX );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2142 FreeFloatMtx( WMMTX2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2143 #endif
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2146 free( gaps );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2147 #if MEMSAVE
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2148 free( aseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2149 free( aseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2150 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2151 FreeCharMtx( aseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2152 FreeCharMtx( aseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2153 #endif
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 return( value );
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2158
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2159
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2160 float Lalignmm_hmout( char seq1, char seq2, double eff1, double eff2, int icyc, int jcyc, int alloclen, char sgap1, char sgap2, char egap1, char egap2, float **map )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2161 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2162 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2163 // int k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2164 int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2165 int ll1, ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2166 int lgth1, lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2167 float wm = 0.0; /* int ?????? */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2168 char **mseq1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2169 char **mseq2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2170 // char **mseq;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2171 float *ogcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2172 float *ogcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2173 float *fgcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2174 float *fgcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2175 float **cpmx1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2176 float **cpmx2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2177 float **gapinfo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2178 // float fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2179 float fpenalty = (float)RNApenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2180 int nglen1, nglen2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2181
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2182
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2183
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2184
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2187 fprintf( stderr, "eff in SA+++align\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2188 for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2189 #endif
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 nglen1 = seqlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2192 nglen2 = seqlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2193
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2194 lgth1 = strlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2195 lgth2 = strlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2196
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2197 ll1 = ( (int)(lgth1) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2198 ll2 = ( (int)(lgth2) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2199
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2200 mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2201 mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2202
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2203 gapinfo = AllocateFloatMtx( 4, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2204 ogcp1 = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2205 ogcp2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2206 fgcp1 = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2207 fgcp2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2208
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 cpmx1 = AllocateFloatMtx( ll1+2, nalphabets+1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2211 cpmx2 = AllocateFloatMtx( ll2+2, nalphabets+1 );
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 for( i=0; i<icyc; i++ )
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( strlen( seq1[i] ) != lgth1 )
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, "i = %d / %d\n", i, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2218 fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2219 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2220 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2221 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2222 for( j=0; j<jcyc; j++ )
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 if( strlen( seq2[j] ) != lgth2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2225 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2226 fprintf( stderr, "j = %d / %d\n", j, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2227 fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2228 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2229 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2230 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2231
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2232 MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2233 MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2234
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2235
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2236 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2237
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2238 if( sgap1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2239 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2240 new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2241 new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2242 new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2243 new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2244 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2245 else
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 st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2248 st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2249 st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2250 st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2251 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2252
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2253 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2254 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2255 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2256 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2257 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2258 // fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
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 for( i=0; i<lgth2; i++ )
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 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2263 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2264 // fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2265 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2266 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2267 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2268 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2269 ogcp1[i] = 0.5 * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2270 fgcp1[i] = 0.5 * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2271 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2272 for( i=0; i<lgth2; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2273 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2274 ogcp2[i] = 0.5 * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2275 fgcp2[i] = 0.5 * fpenalty;
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 #endif
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 gapinfo[0] = ogcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2280 gapinfo[1] = fgcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2281 gapinfo[2] = ogcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2282 gapinfo[3] = fgcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2283 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2284
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2285 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2286 fprintf( stdout, "in MSalignmm.c\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2287 for( i=0; i<icyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2288 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2289 fprintf( stdout, ">%d of GROUP1\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2290 fprintf( stdout, "%s\n", seq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2291 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2292 for( i=0; i<jcyc; i++ )
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( stdout, ">%d of GROUP2\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2295 fprintf( stdout, "%s\n", seq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2296 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2297 fflush( stdout );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2298 #endif
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 wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2301 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2302 fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2303 fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2304 fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2305 fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2306 #endif
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 // fprintf( stderr, "wm = %f\n", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2309
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2310 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2311
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2312 for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2313 for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2314
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2315 if( seqlen( seq1[0] ) != nglen1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2316 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2317 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2318 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2319 exit( 1 );
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 if( seqlen( seq2[0] ) != nglen2 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2322 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2323 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2324 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2325 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2326 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2327
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2328 FreeFloatVec( ogcp1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2329 FreeFloatVec( ogcp2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2330 FreeFloatVec( fgcp1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2331 FreeFloatVec( fgcp2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2332 FreeFloatMtx( cpmx1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2333 FreeFloatMtx( cpmx2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2334 free( (void *)gapinfo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2335
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2336 FreeCharMtx( mseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2337 FreeCharMtx( mseq2 );
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 lgth1 = strlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2340 lgth2 = strlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2341 for( i=0; i<icyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2342 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2343 if( strlen( seq1[i] ) != lgth1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2344 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2345 fprintf( stderr, "i = %d / %d\n", i, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2346 fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2347 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2348 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2349 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2350 for( j=0; j<jcyc; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2351 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2352 if( strlen( seq2[j] ) != lgth2 )
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, "j = %d / %d\n", j, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2355 fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2356 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2357 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2358 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2359
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2360 return( wm );
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
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2363 float Lalign2m2m_hmout( char seq1, char seq2, char seq1r, char seq2r, char dir1, char dir2, double eff1, double eff2, int icyc, int jcyc, int alloclen, char sgap1, char sgap2, char egap1, char egap2, float **map )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2364 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2365 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2366 // int k;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2367 int i, j;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2368 int ll1, ll2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2369 int lgth1, lgth2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2370 float wm = 0.0; /* int ?????? */
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2371 char **mseq1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2372 char **mseq2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2373 float *ogcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2374 float *ogcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2375 float *fgcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2376 float *fgcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2377 float **cpmx1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2378 float **cpmx2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2379 float **gapinfo;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2380 float fpenalty = (float)penalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2381 int nglen1, nglen2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2382
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2383 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2384 fprintf( stderr, "eff in SA+++align\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2385 for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2386 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2387
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2388 nglen1 = seqlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2389 nglen2 = seqlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2390
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2391 lgth1 = strlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2392 lgth2 = strlen( seq2[0] );
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 ll1 = ( (int)(lgth1) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2395 ll2 = ( (int)(lgth2) ) + 100;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2396
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2397 mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2398 mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2399
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2400 gapinfo = AllocateFloatMtx( 4, 0 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2401 ogcp1 = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2402 ogcp2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2403 fgcp1 = AllocateFloatVec( ll1+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2404 fgcp2 = AllocateFloatVec( ll2+2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2405
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2406
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2407 cpmx1 = AllocateFloatMtx( ll1+2, 39 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2408 cpmx2 = AllocateFloatMtx( ll2+2, 39 );
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 for( i=0; i<icyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2411 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2412 if( strlen( seq1[i] ) != lgth1 )
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 fprintf( stderr, "i = %d / %d\n", i, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2415 fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2416 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2417 }
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 for( j=0; j<jcyc; j++ )
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( strlen( seq2[j] ) != lgth2 )
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 fprintf( stderr, "j = %d / %d\n", j, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2424 fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2425 exit( 1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2426 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2427 }
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2430 MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2431 MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2432 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2433 cpmx_ribosum( seq1, seq1r, dir1, cpmx1, eff1, lgth1, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2434 cpmx_ribosum( seq2, seq2r, dir2, cpmx2, eff2, lgth2, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2435 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2436
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2437
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2438 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2439
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2440 if( sgap1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2441 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2442 new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2443 new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2444 new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2445 new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2446 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2447 else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2448 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2449 st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2450 st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2451 st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2452 st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2453 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2454
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2455 #if 1
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2456 for( i=0; i<lgth1; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2457 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2458 ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2459 fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2460 // fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
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<lgth2; 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 ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2465 fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2466 // fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2467 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2468 #else
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2469 for( i=0; i<lgth1; i++ )
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 ogcp1[i] = 0.5 * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2472 fgcp1[i] = 0.5 * fpenalty;
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<lgth2; 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 ogcp2[i] = 0.5 * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2477 fgcp2[i] = 0.5 * fpenalty;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2478 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2479 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2480
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2481 gapinfo[0] = ogcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2482 gapinfo[1] = fgcp1;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2483 gapinfo[2] = ogcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2484 gapinfo[3] = fgcp2;
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2485 #endif
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 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2488 fprintf( stdout, "in MSalignmm.c\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2489 for( i=0; i<icyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2490 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2491 fprintf( stdout, ">%d of GROUP1\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2492 fprintf( stdout, "%s\n", seq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2493 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2494 for( i=0; i<jcyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2495 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2496 fprintf( stdout, ">%d of GROUP2\n", i );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2497 fprintf( stdout, "%s\n", seq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2498 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2499 fflush( stdout );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2500 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2501
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2502 wm = MSalign2m2m_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2503 #if DEBUG
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2504 fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2505 fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2506 fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2507 fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2508 #endif
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 // fprintf( stderr, "wm = %f\n", wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2511
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2512 #if 0
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2513
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2514 for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2515 for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2516
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2517 if( seqlen( seq1[0] ) != nglen1 )
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 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2520 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2521 exit( 1 );
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 if( seqlen( seq2[0] ) != nglen2 )
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 fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2526 exit( 1 );
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 #endif
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2529
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2530 FreeFloatVec( ogcp1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2531 FreeFloatVec( ogcp2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2532 FreeFloatVec( fgcp1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2533 FreeFloatVec( fgcp2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2534 FreeFloatMtx( cpmx1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2535 FreeFloatMtx( cpmx2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2536 free( (void *)gapinfo );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2537
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2538 FreeCharMtx( mseq1 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2539 FreeCharMtx( mseq2 );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2540
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2541 lgth1 = strlen( seq1[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2542 lgth2 = strlen( seq2[0] );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2543 for( i=0; i<icyc; i++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2544 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2545 if( strlen( seq1[i] ) != lgth1 )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2546 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2547 fprintf( stderr, "i = %d / %d\n", i, icyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2548 fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2549 exit( 1 );
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 }
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2552 for( j=0; j<jcyc; j++ )
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2553 {
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2554 if( strlen( seq2[j] ) != lgth2 )
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 fprintf( stderr, "j = %d / %d\n", j, jcyc );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2557 fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2558 exit( 1 );
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 }
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 return( wm );
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty nick parents: diff changeset	2563 }

Mercurial > repos > nick > duplex

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