Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / mafft / core / regtable2seq.c

diff --git a/website/archive/binaries/mac/src/mafft/core/regtable2seq.c b/website/archive/binaries/mac/src/mafft/core/regtable2seq.c
deleted file mode 100644 (file)
index 4251b3b..0000000
--- a/website/archive/binaries/mac/src/mafft/core/regtable2seq.c
+++ /dev/null
@@ -1,212 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-
-char *regfile;
-char *eregfile;
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-    outnumber = 0;
-    inputfile = NULL;
-    regfile = NULL;
-    eregfile = NULL;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-       {
-        while ( (c = *++argv[0]) )
-               {
-            switch( c )
-            {
-                               case 'e':
-                                       eregfile = *++argv;
-                                       fprintf( stderr, "eregfile = %s\n", eregfile );
-                                       --argc;
-                                       goto nextoption;
-                               case 'r':
-                                       regfile = *++argv;
-                                       fprintf( stderr, "regfile = %s\n", regfile );
-                                       --argc;
-                                       goto nextoption;
-                               case 'i':
-                                       inputfile = *++argv;
-                                       fprintf( stderr, "inputfile = %s\n", inputfile );
-                                       --argc;
-                                       goto nextoption;
-                               case 'n' :
-                                       outnumber = 1;
-                                       break;
-                default:
-                    fprintf( stderr, "illegal option %c\n", c );
-                    argc = 0;
-                    break;
-            }
-               }
-               nextoption:
-                       ;
-       }
-    if( argc != 0 ) 
-    {
-        fprintf( stderr, "options: Check source file !\n" );
-        exit( 1 );
-    }
-}
-
-void readereg( FILE *regfp, int **regtable, char **revtable, int *outtable, int *noutpt, int *loutpt )
-{
-       char gett[1000];
-       int j;
-       int mem;
-       char cmem;
-       char reg[5][100];
-       char out[100];
-       int startpos, endpos;
-
-       *noutpt = 0;
-       *loutpt = 0;
-       fgets( gett, 999, regfp );
-       sscanf( gett, "%c %s %s %s %s %s", &cmem, reg[0], reg[1], reg[2], reg[3], reg[4] );
-       if( cmem != 'e' )
-       {
-               fprintf( stderr, "Format error\n" );
-               exit( 1 );
-       }
-       for( j=0; j<5; j++ )
-       {
-               sscanf( reg[j], "%d-%d-%c", regtable[0]+(j*2), regtable[0]+(j*2)+1, revtable[0]+j );
-               fprintf( stderr, "%d %d-%d\n", 0, regtable[0][j*2], regtable[0][j*2+1] );
-               startpos = regtable[0][j*2];
-               endpos   = regtable[0][j*2+1];
-               if( startpos > endpos )
-               {
-                       endpos   = regtable[0][j*2];
-                       startpos = regtable[0][j*2+1];
-               }
-               if( startpos != -1 && endpos != -1 )
-                       *loutpt += endpos - startpos + 1;
-       }
-
-       while( 1 )
-       {
-               fgets( gett, 999, regfp );
-               if( feof( regfp ) ) break;
-               sscanf( gett, "%d o=%s", &mem, out );
-               if( mem >= njob )
-               {
-                       fprintf( stderr, "Out of range\n" );
-                       exit( 1 );
-               }
-               outtable[mem] = atoi( out );
-               if( outtable[mem] ) *noutpt += 1;
-       }
-}
-
-void readreg( FILE *regfp, int **regtable, char **revtable, int *outtable )
-{
-       char gett[1000];
-       int j;
-       int mem;
-       char reg[5][100];
-       char out[100];
-
-       while( 1 )
-       {
-               fgets( gett, 999, regfp );
-               if( feof( regfp ) ) break;
-               sscanf( gett, "%d %s %s %s %s %s o=%s", &mem, reg[0], reg[1], reg[2], reg[3], reg[4], out );
-               if( mem >= njob )
-               {
-                       fprintf( stderr, "Out of range\n" );
-                       exit( 1 );
-               }
-               for( j=0; j<5; j++ )
-               {
-                       sscanf( reg[j], "%d-%d-%c", regtable[mem]+(j*2), regtable[mem]+(j*2)+1, revtable[mem]+j );
-                       fprintf( stderr, "%d %d-%d\n", mem, regtable[mem][j*2], regtable[mem][j*2+1] );
-               }
-               outtable[mem] = atoi( out );
-       }
-}
-
-int main( int argc, char *argv[] )
-{
-       FILE *infp;
-       FILE *regfp;
-       int nlenmin;
-       int **regtable;
-       char **revtable;
-       int *outtable;
-       int i, nout, lout;
-       char **outseq;
-       char **name;
-
-       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_nogap( infp, &nlenmin );
-
-       if( regfile )
-       {
-               regfp = fopen( regfile, "r" );
-               if( !regfp )
-               {
-                       fprintf( stderr, "Cannot open %s\n", regfile );
-                       exit( 1 );
-               }
-               regtable = AllocateIntMtx( njob, 5*2 );
-               revtable = AllocateCharMtx( njob, 5 );
-               outtable = AllocateIntVec( njob );
-               readreg( regfp, regtable, revtable, outtable );
-               cutData( infp, regtable, revtable, outtable );
-       }
-       else if( eregfile )
-       {
-               regfp = fopen( eregfile, "r" );
-               if( !regfp )
-               {
-                       fprintf( stderr, "Cannot open %s\n", eregfile );
-                       exit( 1 );
-               }
-               regtable = AllocateIntMtx( 1, 5*2 );
-               revtable = AllocateCharMtx( 1, 5 );
-               outtable = AllocateIntVec( njob );
-               readereg( regfp, regtable, revtable, outtable, &nout, &lout );
-               fprintf( stderr, "nout = %d, lout = %d\n", nout, lout );
-
-               outseq = AllocateCharMtx( nout, lout+1 );
-               name = AllocateCharMtx( nout, B );
-
-               cutAlignment( infp, regtable, revtable, outtable, name, outseq );
-               fprintf( stderr, "gappick! nout = %d\n", nout );
-               commongappick( nout, outseq );
-               for( i=0; i<nout; i++ )
-               {
-                       fprintf( stdout, "%s\n", name[i] );
-                       fprintf( stdout, "%s\n", outseq[i] );
-               }
-       }
-       else
-       {
-               catData( infp );
-       }
-
-       fprintf( stderr, "Strategy:\n" );
-       fprintf( stderr, " Not-Aligned\n" );
-
-//     fprintf( stdout, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
-       return( 0 );
-}