Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / mafft / core / dndpre2.c

diff --git a/website/archive/binaries/mac/src/mafft/core/dndpre2.c b/website/archive/binaries/mac/src/mafft/core/dndpre2.c
deleted file mode 100644 (file)
index e68a3c3..0000000
--- a/website/archive/binaries/mac/src/mafft/core/dndpre2.c
+++ /dev/null
@@ -1,176 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 1
-
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-       nblosum = 62;
-       fmodel = 0;
-       calledByXced = 0;
-       scoremtx = 0;
-       dorp = NOTSPECIFIED;
-       ppenalty = NOTSPECIFIED;
-       ppenalty_ex = NOTSPECIFIED;
-       poffset = NOTSPECIFIED;
-       kimuraR = NOTSPECIFIED;
-       pamN = NOTSPECIFIED;
-       geta2 = GETA2;
-       fftWinSize = NOTSPECIFIED;
-       fftThreshold = 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 'k':
-                                       kimuraR = atoi( *++argv );
-                                       fprintf( stderr, "kimuraR = %d\n", kimuraR );
-                                       --argc;
-                                       goto nextoption;
-                               case 'b':
-                                       nblosum = atoi( *++argv );
-                                       scoremtx = 1;
-                                       fprintf( stderr, "blosum %d\n", nblosum );
-                                       --argc;
-                                       goto nextoption;
-                               case 'j':
-                                       pamN = atoi( *++argv );
-                                       scoremtx = 0;
-                                       fprintf( stderr, "jtt %d\n", pamN );
-                                       --argc;
-                                       goto nextoption;
-                               case 'm':
-                                       fmodel = 1;
-                                       break;
-                               case 'r':
-                                       fmodel = -1;
-                                       break;
-                               case 'D':
-                                       dorp = 'd';
-                                       break;
-                               case 'P':
-                                       dorp = 'p';
-                                       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 );
-       }
-}
-
-int main( int argc, char *argv[] )
-{
-       static int  nlen[M];    
-       static char name[M][B], **seq;
-       int i, j, alloclen, c;
-       double **mtx;
-       double *self;
-       double tmpdouble;
-       FILE *fp;
-
-       arguments( argc, argv );
-
-       getnumlen( stdin );
-       rewind( stdin );
-
-       if( njob < 2 )
-       {
-               fprintf( stderr, "At least 2 sequences should be input!\n"
-                                                "Only %d sequence found.\n", njob ); 
-               exit( 1 );
-       }
-
-       seq = AllocateCharMtx( njob, nlenmax*9+1 );
-       mtx = AllocateDoubleMtx( njob, njob );
-       self = AllocateDoubleVec( njob );
-       alloclen = nlenmax*9;
-
-       readData( stdin, name, nlen, seq );
-       constants( njob, seq );
-
-
-
-
-       c = seqcheck( seq );
-       if( c )
-       {
-               fprintf( stderr, "Illeagal character %c\n", c );
-               exit( 1 );
-       }
-
-       for( i=0; i<njob; i++ ) 
-       {
-               self[i] = (double)substitution_nid( seq[i], seq[i] );
-//             fprintf( stdout, "self[%d] = %f\n", i, self[i] );
-       }
-
-       for( i=0; i<njob-1; i++ ) 
-               for( j=i+1; j<njob; j++ ) 
-               {
-                       tmpdouble = (double)substitution_score( seq[i], seq[j] );
-//                     fprintf( stdout, "tmpdouble = %f\n", tmpdouble );
-                       mtx[i][j] = ( 1.0 - tmpdouble / MIN( self[i], self[j] ) );
-                       if( mtx[i][j] < 0.95 )
-                               mtx[i][j] = - log( 1.0 - mtx[i][j] );
-                       else
-                               mtx[i][j] = 3.0;
-               }
-       
-#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 );
-       exit( 0 );
-
-       return( 0 );
-}