Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/mafft/core/replaceu.c b/website/archive/binaries/mac/src/mafft/core/replaceu.c
deleted file mode 100644 (file)
index 40be746..0000000
--- a/website/archive/binaries/mac/src/mafft/core/replaceu.c
+++ /dev/null
@@ -1,145 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-
-static int seedoffset;
-
-static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
-{
-       int i;
-       char *pt;
-       for( i=0; i<n; i++ )
-       {
-               pt = seq[i];
-               while( *pt )
-               {
-                       if( !strchr( usual, *pt ) ) *pt = unknown;
-                       else *pt = uporlow( *pt );
-                       pt++;
-               }
-       }
-}
-
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-       seedoffset = 0;
-       inputfile = NULL;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-       {
-        while ( (c = *++argv[0]) )
-               {
-            switch( c )
-            {
-                               case 'o':
-                                       seedoffset = atoi( *++argv );
-                                       fprintf( stderr, "seedoffset = %d\n", seedoffset );
-                                       --argc;
-                                       goto nextoption;
-                               case 'i':
-                                       inputfile = *++argv;
-                                       fprintf( stderr, "inputfile = %s\n", inputfile );
-                                       --argc;
-                                       goto nextoption;
-                default:
-                    fprintf( stderr, "illegal option %c\n", c );
-                    argc = 0;
-                    break;
-            }
-               }
-               nextoption:
-                       ;
-       }
-    if( argc != 0 ) 
-    {
-        fprintf( stderr, "options: Check source file !\n" );
-        exit( 1 );
-    }
-}
-
-
-
-int main( int argc, char *argv[] )
-{
-       FILE *infp;
-       int nlenmin;
-       char **name;
-       char **seq;
-       int *nlen;
-       int i;
-       char *usual;
-
-       arguments( argc, argv );
-
-       if( inputfile )
-       {
-               infp = fopen( inputfile, "r" );
-               if( !infp )
-               {
-                       fprintf( stderr, "Cannot open %s\n", inputfile );
-                       exit( 1 );
-               }
-       }
-       else
-               infp = stdin;
-
-
-       dorp = NOTSPECIFIED;
-       getnumlen_casepreserve( infp, &nlenmin );
-
-       fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
-
-       seq = AllocateCharMtx( njob, nlenmax+1 );
-       name = AllocateCharMtx( njob, B+1 );
-       nlen = AllocateIntVec( njob );
-
-       readData_pointer_casepreserve( infp, name, nlen, seq );
-
-//     for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
-
-#if 0
-       FILE *origfp;
-       origfp = fopen( "_original", "w" );
-       if( !origfp )
-       {
-               fprintf( stderr, "Cannot open _original\n" );
-               exit( 1 );
-       }
-       for( i=0; i<njob; i++ )
-       {
-               nlen[i] = strlen( seq[i] );
-               fprintf( origfp, ">%s\n", name[i]+1 );
-               if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
-               fprintf( origfp, "%s\n", seq[i] );
-       }
-       fclose( origfp );
-#endif
-
-       if( dorp == 'p' )
-       {
-               usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
-               replace_unusual( njob, seq, usual, 'X', toupper );
-       }
-       else
-       {
-               usual = "ATGCUatgcu-";
-               replace_unusual( njob, seq, usual, 'n', tolower );
-       }
-       
-
-
-       for( i=0; i<njob; i++ )
-       {
-               fprintf( stdout, ">%d_oripos_%s\n", i+seedoffset, name[i] );
-               fprintf( stdout, "%s\n", seq[i] );
-       }
-
-       free( nlen );
-       FreeCharMtx( seq );
-       FreeCharMtx( name );
-
-       return( 0 );
-}