source: branches/items/GDE/MAFFT/mafft-7.055-with-extensions/core/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, **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 );
        }

        name = AllocateCharMtx( njob, B+1 );
        seq = AllocateCharMtx( njob, nlenmax*9+1 );
        mtx = AllocateDoubleMtx( njob, njob );
        self = AllocateDoubleVec( njob );
        alloclen = nlenmax*9;

        readData_pointer( 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_pointer( fp, njob, name, mtx );
        fclose( fp );
        exit( 0 );

        return( 0 );
}