Removing old version of mafft to replace with the new

[jabaws.git] / binaries / src / mafft / core / dndpre.c

diff --git a/binaries/src/mafft/core/dndpre.c b/binaries/src/mafft/core/dndpre.c
deleted file mode 100644 (file)
index b9b5f6b..0000000
--- a/binaries/src/mafft/core/dndpre.c
+++ /dev/null
@@ -1,165 +0,0 @@
-#include "mltaln.h"
-
-#define TEST 0
-
-static int treeout = 0;
-
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-       alg = 'X';
-       fmodel = 0;
-       treeout = 0;
-       scoremtx = 1;
-       nblosum = 62;
-       dorp = NOTSPECIFIED;
-       inputfile = NULL;
-       ppenalty = NOTSPECIFIED; //?
-       ppenalty_ex = NOTSPECIFIED; //?
-       poffset = NOTSPECIFIED; //?
-       kimuraR = NOTSPECIFIED;
-       pamN = NOTSPECIFIED;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-       {
-        while ( (c = *++argv[0]) )
-               {
-            switch( c )
-            {
-                               case 't':
-                                       treeout = '1';
-                                       break;
-                               case 'D':
-                                       dorp = 'd';
-                                       break;
-                               case 'a':
-                                       fmodel = 1;
-                                       break;
-                               case 'P':
-                                       dorp = 'p';
-                                       break;
-                               case 'i':
-                                       inputfile = *++argv;
-                                       fprintf( stderr, "inputfile = %s\n", inputfile );
-                                       --argc;
-                                       goto nextoption;
-            }
-               }
-               nextoption:
-                       ;
-       }
-    if( argc != 0 ) 
-       {
-               fprintf( stderr, "options: Check source file !\n" );
-               exit( 1 );
-       }
-}
-
-int main( int argc, char **argv )
-{
-       int i, j;
-       char **seq;
-       static char name[M][B];
-       static int nlen[M];
-       float *selfscore;
-       double **mtx;
-       FILE *fp;
-       FILE *infp;
-       float ssi, ssj, bunbo;
-
-
-       arguments( argc, argv );
-
-       if( inputfile )
-       {
-               infp = fopen( inputfile, "r" );
-               if( !infp )
-               {
-                       fprintf( stderr, "Cannot open %s\n", inputfile );
-                       exit( 1 );
-               }
-       }
-       else
-               infp = stdin;
-
-#if 0
-       PreRead( stdin, &njob, &nlenmax );
-#else
-       getnumlen( infp );
-#endif
-       rewind( infp );
-
-       seq = AllocateCharMtx( njob, nlenmax+1 );
-       mtx = AllocateDoubleMtx( njob, njob );
-       selfscore = AllocateFloatVec( njob );
-
-#if 0
-       FRead( stdin, name, nlen, seq );
-#else
-       readData( infp, name, nlen, seq );
-#endif
-       fclose( infp );
-
-       constants( njob, seq );
-
-#if 0
-       for( i=0; i<njob-1; i++ ) 
-       {
-               fprintf( stderr, "%4d/%4d\r", i+1, njob );
-               for( j=i+1; j<njob; j++ ) 
-                       mtx[i][j] = (double)substitution_hosei( seq[i], seq[j] );
-//                     fprintf( stderr, "i=%d,j=%d, l=%d &&&  %f\n", i, j, nlen[0], mtx[i][j] );
-       }
-#else // 061003
-       for( i=0; i<njob; i++ )
-       {
-               selfscore[i] = (float)naivepairscore11( seq[i], seq[i], penalty );
-
-       }
-       for( i=0; i<njob-1; i++ )
-       {
-               ssi = selfscore[i];
-               fprintf( stderr, "%4d/%4d\r", i+1, njob );
-               for( j=i+1; j<njob; j++ )
-               {
-                       ssj = selfscore[j];
-                       bunbo = MIN( ssi, ssj );
-                       if( bunbo == 0.0 )
-                               mtx[i][j] = 1.0;
-                       else
-                               mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
-//                             mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
-//                     fprintf( stderr, "i=%d,j=%d, l=%d### %f, score = %d\n", i, j, nlen[0], mtx[i][j], naivepairscore11( seq[i], seq[j], penalty )  );
-               }
-       }
-#endif
-       
-#if TEST
-       for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) 
-               fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
-#endif
-
-       fp = fopen( "hat2", "w" );
-       WriteHat2( fp, njob, name, mtx );
-       fclose( fp );
-#if 0
-       if( treeout )
-       {
-               int ***topol;
-               double **len;
-
-               topol = AllocateIntCub( njob, 2, njob );
-               len = AllocateDoubleMtx( njob, njob );
-               veryfastsupg_double_outtree( njob, mtx, topol, len );
-       }
-#endif
-       SHOWVERSION;
-       exit( 0 );
-/*
-       res = system( ALNDIR "/spgsdl < hat2"  );
-       if( res ) exit( 1 );
-       else exit( 0 );
-*/
-}