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Sourcecode: mafft version File versions  Download package

dndpre2.c

#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 );
}

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