X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2Fmltaln.h;fp=binaries%2Fsrc%2Fmafft%2Fcore%2Fmltaln.h;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=bfad0abb8c96aac1e8922ea863192eb602cb16c5;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git diff --git a/binaries/src/mafft/core/mltaln.h b/binaries/src/mafft/core/mltaln.h deleted file mode 100644 index bfad0ab..0000000 --- a/binaries/src/mafft/core/mltaln.h +++ /dev/null @@ -1,268 +0,0 @@ -#define USE_XCED 0 - -#if USE_XCED -#include "config.h" -#include "share.h" -#else -#endif - -#include -#include -#include -#include -#include -#include -#include -#include -#include "mtxutl.h" -#include - -#define VERSION "6.713b" -#define SHOWVERSION fprintf( stderr, "%s (%s) Version " VERSION " alg=%c, model=%s\n", progName( argv[0] ), (dorp=='d')?"nuc":"aa", alg, modelname ) - -#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 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; - - -#include "fft.h" -#include "dp.h" -#include "functions.h" -