--- /dev/null
+#define USE_XCED 0
+
+#if USE_XCED
+#include "config.h"
+#include "share.h"
+#else
+#endif
+
+#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>
+#ifdef enablemultithread
+#include <pthread.h>
+#endif
+
+#define VERSION "6.857b"
+#define SHOWVERSION fprintf( stderr, "%s (%s) Version " VERSION " alg=%c, model=%s\n%d thread(s)\n", progName( argv[0] ), (dorp=='d')?"nuc":"aa", alg, modelname, 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 50000 /* 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[100];
+extern int njob, nlenmax;
+extern int amino_n[0x80];
+extern char amino_grp[0x80];
+extern int amino_dis[0x80][0x80];
+extern int amino_disLN[0x80][0x80];
+extern double amino_dis_consweight_multi[0x80][0x80];
+extern int n_dis[26][26];
+extern int n_disFFT[26][26];
+extern float n_dis_consweight_multi[26][26];
+extern char amino[26];
+extern double polarity[20];
+extern double volume[20];
+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 penalty, ppenalty, penaltyLN;
+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 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();
+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;
+} Treedep;
+
+
+#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 outnumber;
+
+extern char *newgapstr;
git://source.jalview.org / jabaws.git / blobdiff