Delete unneeded directory
[jabaws.git] / website / archive / binaries / mac / src / mafft / core / getlag.c
diff --git a/website/archive/binaries/mac/src/mafft/core/getlag.c b/website/archive/binaries/mac/src/mafft/core/getlag.c
deleted file mode 100644 (file)
index d37c2d8..0000000
+++ /dev/null
@@ -1,461 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-       calledByXced = 0;
-       devide = 0;
-       use_fft = 0;
-       fftscore = 1;
-       fftRepeatStop = 0;
-       fftNoAnchStop = 0;
-    weight = 3;
-    utree = 1;
-       tbutree = 1;
-    refine = 0;
-    check = 1;
-    cut = 0.0;
-    disp = 0;
-    outgap = 1;
-    alg = 'C';
-    mix = 0;
-       tbitr = 0;
-       scmtd = 5;
-       tbweight = 0;
-       tbrweight = 3;
-       checkC = 0;
-       treemethod = 'x';
-       contin = 0;
-       ppenalty = NOTSPECIFIED;
-       ppenalty_ex = NOTSPECIFIED;
-       poffset = NOTSPECIFIED;
-       kimuraR = NOTSPECIFIED;
-       pamN = NOTSPECIFIED;
-       geta2 = GETA2;
-       scoremtx = NOTSPECIFIED;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-       {
-        while ( (c = *++argv[0]) )
-               {
-            switch( c )
-            {
-                               case 'f':
-                                       ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
-                                       fprintf( stderr, "ppenalty = %d\n", ppenalty );
-                                       --argc;
-                                       goto nextoption;
-                               case 'g':
-                                       ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
-                                       fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
-                                       --argc;
-                                       goto nextoption;
-                               case 'h':
-                                       poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
-                                       fprintf( stderr, "poffset = %d\n", poffset );
-                                       --argc;
-                                       goto nextoption;
-                               case 'D':
-                                       scoremtx = -1;
-                                       break;
-                               case 'P':
-                                       scoremtx = 0;
-                                       break;
-                               case 'i':
-                                       contin = 1;
-                                       break;
-                               case 'e':
-                                       fftscore = 0;
-                                       break;
-                               case 'O':
-                                       fftNoAnchStop = 1;
-                                       break;
-                               case 'R':
-                                       fftRepeatStop = 1;
-                                       break;
-                               case 'Q':
-                                       calledByXced = 1;
-                                       break;
-                               case 's':
-                                       treemethod = 's';
-                                       break;
-                               case 'x':
-                                       treemethod = 'x';
-                                       break;
-                               case 'p':
-                                       treemethod = 'p';
-                                       break;
-                               case 'a':
-                                       alg = 'a';
-                                       break;
-                               case 'A':
-                                       alg = 'A';
-                                       break;
-                               case 'S':
-                                       alg = 'S';
-                                       break;
-                               case 'C':
-                                       alg = 'C';
-                                       break;
-                               case 'F':
-                                       use_fft = 1;
-                                       break;
-                               case 'v':
-                                       tbrweight = 3;
-                                       break;
-                               case 'd':
-                                       disp = 1;
-                                       break;
-                               case 'o':
-                                       outgap = 0;
-                                       break;
-/* Modified 01/08/27, default: user tree */
-                               case 'J':
-                                       tbutree = 0;
-                                       break;
-/* modification end. */
-                               case 'Z':
-                                       checkC = 1;
-                                       break;
-                default:
-                    fprintf( stderr, "illegal option %c\n", c );
-                    argc = 0;
-                    break;
-            }
-               }
-               nextoption:
-                       ;
-       }
-    if( argc == 1 )
-    {
-        cut = atof( (*argv) );
-        argc--;
-    }
-    if( argc != 0 ) 
-    {
-        fprintf( stderr, "options: Check source file !\n" );
-        exit( 1 );
-    }
-       if( tbitr == 1 && outgap == 0 )
-       {
-               fprintf( stderr, "conflicting options : o, m or u\n" );
-               exit( 1 );
-       }
-       if( alg == 'C' && outgap == 0 )
-       {
-               fprintf( stderr, "conflicting options : C, o\n" );
-               exit( 1 );
-       }
-       readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
-}
-
-
-void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
-{
-       int i, j, l;
-       int clus1, clus2;
-       int s1, s2, r1, r2;
-       float pscore;
-       static char *indication1, *indication2;
-       static char **name1, **name2;
-       static double **partialmtx = NULL;
-       static int ***partialtopol = NULL;
-       static double **partiallen = NULL;
-       static double **partialeff = NULL;
-       static double *effarr = NULL;
-       static double *effarr1 = NULL;
-       static double *effarr2 = NULL;
-#if 0
-       char pair[njob][njob];
-#else
-       static char **pair;
-#endif
-       if( partialtopol == NULL ) 
-       {
-               partialmtx = AllocateDoubleMtx( njob, njob );
-               partialtopol = AllocateIntCub( njob, 2, njob );
-               partialeff = AllocateDoubleMtx( njob, njob );
-               partiallen = AllocateDoubleMtx( njob, 2 );
-               effarr = AllocateDoubleVec( njob );
-               effarr1 = AllocateDoubleVec( njob );
-               effarr2 = AllocateDoubleVec( njob );
-               indication1 = AllocateCharVec( njob*3+100 );
-               indication2 = AllocateCharVec( njob*3+100 );
-               name1 = AllocateCharMtx( njob, B+1 );
-               name2 = AllocateCharMtx( njob, B+1 );
-#if 0
-#else
-               pair = AllocateCharMtx( njob, njob );
-#endif
-       }
-
-       if( checkC )
-               for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );
-
-       for( i=0; i<njob; i++ ) effarr[i] = eff[i][i];
-       for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
-
-       if( checkC )
-               for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );
-
-       writePre( njob, name, nlen, aseq, 0 );
-
-       for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
-       for( i=0; i<njob; i++ ) pair[i][i] = 1;
-       for( l=0; l<njob-1; l++ )
-       {
-               s1 = topol[l][0][0];
-               for( i=0; (r1=topol[l][0][i])>-1; i++ ) 
-                       if( pair[s1][r1] != 1 ) exit( 1 );
-               s2 = topol[l][1][0];
-               for( i=0; (r2=topol[l][1][i])>-1; i++ ) 
-                       if( pair[s2][r2] != 1 ) exit( 1 );
-
-               clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
-               clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
-               fprintf( trap_g, "\nSTEP-%d\n", l );
-               fprintf( trap_g, "group1 = %s\n", indication1 );
-               fprintf( trap_g, "group2 = %s\n", indication2 );
-
-               fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
-               fprintf( stderr, "group1 = %.66s", indication1 );
-               if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
-               fprintf( stderr, "\n" );
-               fprintf( stderr, "group2 = %.66s", indication2 );
-               if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
-               fprintf( stderr, "\n" );
-
-               if( checkC )
-                       for( i=0; i<clus1; i++ ) fprintf( stderr, "STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
-/*
-               fprintf( stderr, "before align all\n" );
-               display( aseq, njob );
-               fprintf( stderr, "\n" );
-               fprintf( stderr, "before align 1 %s \n", indication1 );
-               display( mseq1, clus1 );
-               fprintf( stderr, "\n" );
-               fprintf( stderr, "before align 2 %s \n", indication2 );
-               display( mseq2, clus2 );
-               fprintf( stderr, "\n" );
-*/
-
-               pscore = Fgetlag( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
-
-               for( i=0; (r2=topol[l][1][i])>-1; i++ ) 
-               {
-                       pair[s1][r2] = 1;
-                       pair[s2][r2] = 0;
-               }
-
-               writePre( njob, name, nlen, aseq, 0 );
-
-               if( disp ) display( aseq, njob );
-               fprintf( stderr, "\n" );
-
-       }
-}
-
-static void WriteOptions( FILE *fp )
-{
-       fprintf( fp, "tree-base method\n" );
-       if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
-       else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
-       if( tbitr || tbweight ) 
-       {
-               fprintf( fp, "iterate at each step\n" );
-               if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" ); 
-               if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" ); 
-               if( tbweight ) fprintf( fp, "  weighted\n" ); 
-               fprintf( fp, "\n" );
-       }
-       if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
-       else if( scoremtx ==  1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
-       else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
-       else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
-
-    if( scoremtx == 0 || scoremtx == -1 )
-        fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-    else
-        fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );
-
-       if( alg == 'a' )
-               fprintf( fp, "Algorithm A\n" );
-       else if( alg == 'A' ) 
-               fprintf( fp, "Apgorithm A+\n" );
-       else if( alg == 'S' ) 
-               fprintf( fp, "Apgorithm S\n" );
-       else if( alg == 'C' ) 
-               fprintf( fp, "Apgorithm A+/C\n" );
-       else
-               fprintf( fp, "Unknown algorithm\n" );
-
-       if( treemethod == 'x' )
-               fprintf( fp, "Tree = UPGMA (3).\n" );
-       else if( treemethod == 's' )
-               fprintf( fp, "Tree = UPGMA (2).\n" );
-       else if( treemethod == 'p' )
-               fprintf( fp, "Tree = UPGMA (1).\n" );
-       else
-               fprintf( fp, "Unknown tree.\n" );
-
-    if( use_fft )
-    {
-        fprintf( fp, "FFT on\n" );
-        if( scoremtx == -1 )
-            fprintf( fp, "Basis : 4 nucleotides\n" );
-        else
-        {
-            if( fftscore )
-                fprintf( fp, "Basis : Polarity and Volume\n" );
-            else
-                fprintf( fp, "Basis : 20 amino acids\n" );
-        }
-        fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
-        fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
-    }
-       else
-        fprintf( fp, "FFT off\n" );
-       fflush( fp );
-}
-        
-
-int main( int argc, char *argv[] )
-{
-       static int  nlen[M];    
-       static char **name, **seq;
-       static char **mseq1, **mseq2;
-       static char **aseq;
-       static char **bseq;
-       static double **pscore;
-       static double **eff;
-       static double **node0, **node1;
-       int i, j;
-       static int ***topol;
-       static double **len;
-       FILE *prep;
-       char c;
-       int alloclen;
-
-       arguments( argc, argv );
-       getnumlen( stdin );
-       rewind( stdin );
-
-       name = AllocateCharMtx( njob, B+1 );
-       seq = AllocateCharMtx( njob, nlenmax*5+1 );
-       aseq = AllocateCharMtx( njob, nlenmax*5+1 );
-       bseq = AllocateCharMtx( njob, nlenmax*5+1 );
-       mseq1 = AllocateCharMtx( njob, 0 );
-       mseq2 = AllocateCharMtx( njob, 0 );
-       alloclen = nlenmax*5;
-
-       topol = AllocateIntCub( njob, 2, njob );
-       len = AllocateDoubleMtx( njob, 2 );
-       pscore = AllocateDoubleMtx( njob, njob );
-       eff = AllocateDoubleMtx( njob, njob );
-       node0 = AllocateDoubleMtx( njob, njob );
-       node1 = AllocateDoubleMtx( njob, njob );
-
-#if 0
-       Read( name, nlen, seq );
-#else
-       readData_pointer( stdin, name, nlen, seq );
-#endif
-
-       constants( njob, seq );
-
-#if 0
-       fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
-#endif
-
-       initSignalSM();
-
-       initFiles();
-
-       WriteOptions( trap_g );
-
-       c = seqcheck( seq );
-       if( c )
-       {
-               fprintf( stderr, "Illeagal character %c\n", c );
-               exit( 1 );
-       }
-
-       writePre( njob, name, nlen, seq, 0 );
-
-       if( tbutree == 0 )
-       {
-               for( i=1; i<njob; i++ ) 
-               {
-                       if( nlen[i] != nlen[0] ) 
-                       {
-                               fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
-                               exit( 1 );
-                       }
-               }
-               for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) 
-               {
-               /*
-                       pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
-               */
-                       pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
-               }
-       }
-       else
-       {
-               fprintf( stderr, "Loading 'hat2' ... " );
-               prep = fopen( "hat2", "r" );
-               if( prep == NULL ) ErrorExit( "Make hat2." );
-               readhat2_pointer( prep, njob, name, pscore );
-               fclose( prep );
-               fprintf( stderr, "done.\n" );
-
-#if 0
-               prep = fopen( "hat2_check", "w" );
-               WriteHat2( prep, njob, name, pscore );
-               fclose( prep );
-#endif
-
-       }
-
-       fprintf( stderr, "Constructing dendrogram ... " );
-       if( treemethod == 'x' )
-               supg( njob, pscore, topol, len );
-       else if( treemethod == 's' )
-               spg( njob, pscore, topol, len );
-       else if( treemethod == 'p' )
-               upg2( njob, pscore, topol, len );
-       else 
-               ErrorExit( "Incorrect tree\n" );
-       fprintf( stderr, "done.\n" );
-
-       countnode( njob, topol, node0 );
-       if( tbrweight )
-       {
-               weight = 3; 
-               utree = 0; counteff( njob, topol, len, eff ); utree = 1;
-       }
-       else
-       {
-               for( i=0; i<njob; i++ ) eff[i][i] = 1.0;
-       }
-
-
-       for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
-       treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );
-
-       fprintf( trap_g, "done\n" );
-       fclose( trap_g );
-
-       writePre( njob, name, nlen, aseq, !contin );
-       writeData_pointer( stdout, njob, name, nlen, aseq );
-#if IODEBUG
-       fprintf( stderr, "OSHIMAI\n" );
-#endif
-       SHOWVERSION;
-       return( 0 );
-}