Removing old version of mafft to replace with the new

[jabaws.git] / binaries / src / mafft / core / mltaln.h.save

diff --git a/binaries/src/mafft/core/mltaln.h.save b/binaries/src/mafft/core/mltaln.h.save
deleted file mode 100644 (file)
index 842a7b0..0000000
--- a/binaries/src/mafft/core/mltaln.h.save
+++ /dev/null
@@ -1,217 +0,0 @@
-#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"
-
-#define SHOWVERSION fprintf( stderr, "%s (%s) Version 5.571, model=%s\n", progName( argv[0] ), (dorp=='d')?"nuc":"aa", modelname )
-
-#define FFT_THRESHOLD  70
-#define FFT_WINSIZE_P   20
-#define FFT_WINSIZE_D   100
-#define DISPSEQF  60
-#define DISPSITEI    0
-#define MAXITERATION 500
-#define M   10000       /* njob no saidaiti */
-#define N  500000       /* 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
-
-char modelname[100];
-int njob, nlenmax;
-int amino_n[0x80];
-char amino_grp[0x80];
-int amino_dis[0x80][0x80];
-int n_dis[26][26];
-char amino[26];
-double polarity[20];
-double volume[20];
-
-int ppid;
-double fastathreshold;
-int pslocal, ppslocal;
-int constraint;
-int divpairscore;
-int fmodel; // 1-> fmodel 0->default -1->raw
-int nblosum; // 45, 50, 62, 80
-int kobetsubunkatsu;
-int dorp;
-int niter;
-int contin;
-int calledByXced;
-int devide;
-int scmtd;
-int weight;
-int utree;
-int tbutree;
-int refine;
-int check;
-double cut;
-int cooling;
-int penalty, ppenalty;
-int penalty_ex, ppenalty_ex;
-int offset, poffset;
-int scoremtx;
-int TMorJTT;
-char use_fft;
-int fftscore;
-int fftWinSize;
-int fftThreshold;
-int fftRepeatStop;
-int fftNoAnchStop;
-int divWinSize;
-int divThreshold;
-int disp;
-int outgap;
-char alg;
-int cnst;
-int mix;
-int tbitr;
-int tbweight;
-int tbrweight;
-int disopt;
-int pamN;
-int checkC;
-float geta2;
-int treemethod;
-int kimuraR;
-char *swopt;
-int fftkeika;
-int score_check;
-int makedistmtx;
-char *inputfile;
-
-char *signalSM;
-FILE *prep_g;
-FILE *trap_g;
-
-/* 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
-{
-       struct _LocalHom *next;
-       int start1;
-       int end1;
-       int start2;
-       int end2;
-       double opt;
-       int overlapaa;
-       double importance;
-       double wimportance;
-} 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 _Achain
-{
-       int next;
-       int prev;
-//     int curr;
-} Achain;
-
-char **seq_g;
-char **res_g;
-
-typedef struct _Fukusosuu
-{
-    double R;
-    double I;
-} Fukusosuu;
-
-#include "fft.h"
-#include "functions.h"