diff mafft/core/mltaln.h @ 18:e4d75f9efb90 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/mltaln.h	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,328 @@
+#define USE_XCED 0
+
+#if USE_XCED
+#include "config.h"
+#include "share.h"
+#else
+#endif
+
+#include "mafft.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <stddef.h>
+#include <sys/types.h>
+#include <string.h>
+#include <unistd.h>
+#include <math.h>
+#include <ctype.h>
+#include "mtxutl.h"
+#include <float.h>
+#include <stdarg.h>
+#ifdef enablemultithread
+#include <pthread.h>
+#endif
+
+#define VERSION "7.221"
+#define SHOWVERSION reporterr( "%s (%s) Version " VERSION " alg=%c, model=%s, amax=%3.1f\n%d thread(s)\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )
+
+#define FFT_THRESHOLD  80
+#define FFT_WINSIZE_P   20
+#define FFT_WINSIZE_D   100
+#define DISPSEQF  60
+#define DISPSITEI    0
+#define MAXITERATION 500
+#define M  500000       /* njob no saidaiti */
+#define N 5000000       /* nlen no saidaiti */
+#define MAXSEG 100000
+#define B     256
+#define C     60       /*  1 gyou no mojisuu */
+#define D      6
+#define rnd() ( ( 1.0 / ( RAND_MAX + 1.0 ) ) * rand() )
+#define MAX(X,Y)    ( ((X)>(Y))?(X):(Y) )
+#define MIN(X,Y)    ( ((X)<(Y))?(X):(Y) )
+#define G(X)        ( ((X)>(0))?(X):(0) )
+#define BEFF   1.0   /* 0.6 ni suruto zureru */
+#define WIN   3
+#define SGAPP -1000
+#define GETA2 0.001
+#define GETA3 0.001
+#define NOTSPECIFIED  100009
+#define SUEFF   0.1  /* upg/(spg+upg)  -> sueff.sed */ 
+#define DIVLOCAL 0
+#define INTMTXSCALE 1000000.0
+#define JTT 201
+#define TM  202
+
+extern char modelname[500];
+extern int njob, nlenmax;
+extern int amino_n[0x80];
+extern char amino_grp[0x80];
+extern int amino_dis[0x80][0x80];
+extern double **n_disLN;
+extern double amino_dis_consweight_multi[0x80][0x80];
+extern int **n_dis;
+extern int **n_disFFT;
+extern double **n_dis_consweight_multi;
+extern char amino[0x80];
+extern double polarity[0x80];
+extern double volume[0x80];
+extern int ribosumdis[37][37];
+
+extern int ppid;
+extern double thrinter;
+extern double fastathreshold;
+extern int pslocal, ppslocal;
+extern int constraint;
+extern int divpairscore;
+extern int fmodel; // 1-> fmodel 0->default -1->raw
+extern int nblosum; // 45, 50, 62, 80
+extern int kobetsubunkatsu;
+extern int bunkatsu;
+extern int dorp;
+extern int niter;
+extern int contin;
+extern int calledByXced;
+extern int devide;
+extern int scmtd;
+extern int weight;
+extern int utree;
+extern int tbutree;
+extern int refine;
+extern int check;
+extern double cut;
+extern int cooling;
+extern int trywarp;
+extern int penalty, ppenalty, penaltyLN;
+extern int penalty_dist, ppenalty_dist;
+extern int RNApenalty, RNAppenalty;
+extern int RNApenalty_ex, RNAppenalty_ex;
+extern int penalty_ex, ppenalty_ex, penalty_exLN;
+extern int penalty_EX, ppenalty_EX;
+extern int penalty_OP, ppenalty_OP;
+extern int penalty_shift;
+extern double penalty_shift_factor;
+extern int offset, poffset, offsetLN, offsetFFT;
+extern int RNAthr, RNApthr;
+extern int scoremtx;
+extern int TMorJTT;
+extern char use_fft;
+extern char force_fft;
+extern int nevermemsave;
+extern int fftscore;
+extern int fftWinSize;
+extern int fftThreshold;
+extern int fftRepeatStop;
+extern int fftNoAnchStop;
+extern int divWinSize;
+extern int divThreshold;
+extern int disp;
+extern int outgap;
+extern char alg;
+extern int cnst;
+extern int mix;
+extern int tbitr;
+extern int tbweight;
+extern int tbrweight;
+extern int disopt;
+extern int pamN;
+extern int checkC;
+extern float geta2;
+extern int treemethod;
+extern int kimuraR;
+extern char *swopt;
+extern int fftkeika;
+extern int score_check;
+extern char *inputfile;
+extern char *addfile;
+extern int addprofile;
+extern float consweight_multi;
+extern float consweight_rna;
+extern char RNAscoremtx;
+
+extern char *signalSM;
+extern FILE *prep_g;
+extern FILE *trap_g;
+extern char **seq_g;
+extern char **res_g;
+extern int rnakozo;
+extern char rnaprediction;
+
+/* sengen no ichi ha koko dake de ha nai */
+extern void constants();
+extern char **Calignm1();
+extern char **Dalignm1();
+extern char **align0();
+extern double Cscore_m_1( char **, int, int, double ** );
+extern double score_m_1(  char **, int, int, double ** );
+extern double score_calc0( char **, int, double **, int );
+extern char seqcheck( char ** );
+extern float substitution( char *, char * );
+extern float substitution_score( char *, char * );
+extern float substitution_nid( char *, char * );
+extern float substitution_hosei( char *, char * );
+extern double ipower( double, int );
+extern float translate_and_Calign();
+extern float A__align();
+extern float A__align11();
+extern float A__align_gapmap();
+extern float partA__align();
+extern float L__align11( double **scoringmtx, float scoreoffset, char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
+extern float G__align11();
+extern float Falign();
+extern float Falign_localhom();
+extern float Conalign();
+extern float Aalign();
+extern float imp_match_out_sc( int, int );
+extern float part_imp_match_out_sc( int, int );
+extern void ErrorExit();
+extern void cpmx_calc();
+extern void intergroup_score( char **, char **, double *, double *, int, int, int, double * );
+extern int conjuctionfortbfast();
+extern int fastconjuction();
+extern char seqcheck( char ** );
+
+typedef struct _LocalHom
+{
+	int nokori;
+	struct _LocalHom *next;
+	struct _LocalHom *last;
+	int start1;
+	int end1;
+	int start2;
+	int end2;
+	double opt;
+	int overlapaa;
+	int extended;
+	double importance;
+	float fimportance;
+	double wimportance;
+	char korh;
+} LocalHom;
+
+typedef struct _NodeInCub
+{
+	int step;
+	int LorR;
+} NodeInCub;
+
+typedef struct _Node
+{
+	struct _Node *children[3];
+	int tmpChildren[3];
+	double length[3];
+	double *weightptr[3];
+	int top[3];
+	int *members[3];
+} Node;
+
+typedef struct _Segment
+{
+	int start;
+	int end;
+	int center;
+	double score;
+	int skipForeward;
+	int skipBackward;
+	struct _Segment *pair;
+	int  number;
+} Segment;
+
+typedef struct _Segments
+{
+	Segment group1;
+	Segment group2;
+	int number1;
+	int number2;
+} Segments;
+
+typedef struct _Bchain
+{
+	struct _Bchain *next;
+	struct _Bchain *prev;
+	int pos;
+} Bchain;
+
+typedef struct _Achain
+{
+	int next;
+	int prev;
+//	int curr;
+} Achain;
+
+
+typedef struct _Fukusosuu
+{
+    double R;
+    double I;
+} Fukusosuu;
+
+typedef struct _Gappattern
+{
+	int len;
+	float freq;
+} Gappat;
+
+typedef struct _RNApair
+{
+	int uppos;
+	float upscore;
+	int downpos;
+	float downscore;
+	int bestpos;
+	float bestscore;
+} RNApair;
+
+typedef struct _Treedep
+{
+	int child0;
+	int child1;
+	int done;
+	float distfromtip;
+} Treedep;
+
+typedef struct _Addtree
+{
+	int nearest;
+	float dist1;
+	char *neighbors;
+	float dist2;
+} Addtree;
+
+#include "fft.h"
+#include "dp.h"
+#include "functions.h"
+
+#ifdef enablemultithread
+#define TLS __thread
+#else
+#define TLS 
+#endif
+
+extern TLS int commonAlloc1;
+extern TLS int commonAlloc2;
+extern TLS int **commonIP;
+extern TLS int **commonJP;
+extern int nthread;
+extern int randomseed;
+extern int parallelizationstrategy;
+#define BESTFIRST 0
+#define BAATARI0 1
+#define BAATARI1 2
+#define BAATARI2 3
+
+extern int scoreout;
+extern int spscoreout;
+extern int outnumber;
+
+extern int legacygapcost;
+
+extern TLS char *newgapstr;
+
+extern int nalphabets;
+extern int nscoredalphabets;
+extern double specificityconsideration;
+extern int ndistclass, maxdistclass;
+
+extern int gmsg;
+
+extern double sueff_global;