+++ /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