binaries/src/mafft/core/score.c

   1 #include "mltaln.h"
   2
   3 #define DEBUG 0
   4
   5 void arguments( int argc, char *argv[] )
   6 {
   7     int c;
   8
   9         ppenalty = NOTSPECIFIED;
  10         ppenalty_ex = NOTSPECIFIED;
  11         poffset = NOTSPECIFIED;
  12         kimuraR = NOTSPECIFIED;
  13         pamN = NOTSPECIFIED;
  14         scoremtx = NOTSPECIFIED;
  15
  16     while( --argc > 0 && (*++argv)[0] == '-' )
  17         {
  18         while ( ( c = *++argv[0] ) )
  19                 {
  20             switch( c )
  21             {
  22                                 case 'f':
  23                                         ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
  24                                         fprintf( stderr, "ppenalty = %d\n", ppenalty );
  25                                         --argc;
  26                                         goto nextoption;
  27                                 case 'g':
  28                                         ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
  29                                         fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
  30                                         --argc;
  31                                         goto nextoption;
  32                                 case 'h':
  33                                         poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
  34                                         fprintf( stderr, "poffset = %d\n", poffset );
  35                                         --argc;
  36                                         goto nextoption;
  37                                 case 'k':
  38                                         kimuraR = atoi( *++argv );
  39                                         fprintf( stderr, "kimuraR = %d\n", kimuraR );
  40                                         --argc;
  41                                         goto nextoption;
  42                                 case 'D':
  43                                         scoremtx = -1;
  44                                         break;
  45                                 case 'P':
  46                                         scoremtx = 0;
  47                                         break;
  48                 default:
  49                     fprintf( stderr, "illegal option %c\n", c );
  50                     argc = 0;
  51                     break;
  52             }
  53                 }
  54                 nextoption:
  55                         ;
  56         }
  57     if( argc == 1 )
  58     {
  59         cut = atof( (*argv) );
  60         argc--;
  61     }
  62 }
  63
  64
  65 int main( int ac, char **av )
  66 {
  67         int nlen[M];
  68         static char name[M][B], **seq;
  69         double score;
  70         extern double score_calc_for_score( int, char ** );
  71
  72         arguments( ac, av );
  73
  74         getnumlen( stdin );
  75         rewind( stdin );
  76
  77         seq = AllocateCharMtx( njob, nlenmax );
  78
  79         readData( stdin, name, nlen, seq );
  80
  81         if( !isaligned( njob, seq ) ) ErrorExit( "Not aligned." );
  82
  83         constants( njob, seq );
  84
  85         score = score_calc_for_score( njob, seq );
  86         if( scoremtx == 0 ) score += offset;
  87
  88         fprintf( stdout, "score = %f\n", score );
  89         if     ( scoremtx ==  0 ) fprintf( stdout, "JTT %dPAM\n", pamN );
  90         else if( scoremtx ==  1 ) fprintf( stdout, "Dayhoff( machigai ga aru )\n" );
  91         else if( scoremtx ==  2 ) fprintf( stdout, "M-Y\n" );
  92         else if( scoremtx == -1 ) fprintf( stdout, "DNA 1:%d\n", kimuraR );
  93
  94         fprintf( stdout, "gap penalty = %+6.2f, %+6.2f, %+6.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
  95         exit( 0 );
  96 }