binaries/src/mafft/core/seq2regtable.c

   1 #include "mltaln.h"
   2
   3 #define DEBUG 0
   4
   5 char *weboutfile = NULL;
   6
   7
   8 void arguments( int argc, char *argv[] )
   9 {
  10     int c;
  11
  12     while( --argc > 0 && (*++argv)[0] == '-' )
  13         {
  14         while ( (c = *++argv[0]) )
  15                 {
  16             switch( c )
  17             {
  18                                 case 'i':
  19                                         inputfile = *++argv;
  20                                         fprintf( stderr, "inputfile = %s\n", inputfile );
  21                                         --argc;
  22                                         goto nextoption;
  23                                 case 'w':
  24                                         weboutfile = *++argv;
  25                                         fprintf( stderr, "weboutfile = %s\n", weboutfile );
  26                                         --argc;
  27                                         goto nextoption;
  28                 default:
  29                     fprintf( stderr, "illegal option %c\n", c );
  30                     argc = 0;
  31                     break;
  32             }
  33                 }
  34                 nextoption:
  35                         ;
  36         }
  37     if( argc != 0 )
  38     {
  39         fprintf( stderr, "options: Check source file !\n" );
  40         exit( 1 );
  41     }
  42 }
  43
  44
  45 int main( int argc, char *argv[] )
  46 {
  47         FILE *infp;
  48         FILE *weboutfp;
  49         int nlenmin;
  50         int isaligned = 0;
  51
  52         arguments( argc, argv );
  53
  54         if( inputfile )
  55         {
  56                 infp = fopen( inputfile, "r" );
  57                 if( !infp )
  58                 {
  59                         fprintf( stderr, "Cannot open %s\n", inputfile );
  60                         exit( 1 );
  61                 }
  62         }
  63         else
  64                 infp = stdin;
  65
  66         if( weboutfile )
  67         {
  68                 weboutfp = fopen( weboutfile, "w" );
  69                 if( !weboutfp )
  70                 {
  71                         fprintf( stderr, "Cannot open %s\n", weboutfp );
  72                         exit( 1 );
  73                 }
  74         }
  75
  76         dorp = NOTSPECIFIED;
  77         if( weboutfile )
  78         {
  79                 getnumlen_nogap_outallreg_web( infp, weboutfp, &nlenmin, &isaligned );
  80                 if( isaligned ) fprintf( stdout, "Aligned\n" );
  81                 else fprintf( stdout, "Not aligned\n" );
  82         }
  83         else
  84                 getnumlen_nogap_outallreg( infp, &nlenmin );
  85
  86 }