source: branches/lib/GDE/MAFFT/mafft-7.055-with-extensions/core/dndpre_score.c

#include "mltaln.h"

#define TEST 0

int main()
{
        int i, j;
        char **seq;
        static char name[M][B];
        static int nlen[M];
        double **mtx;
        FILE *fp;
        int res;

        scoremtx = NOTSPECIFIED;

#if 0
        PreRead( stdin, &njob, &nlenmax );
#else
        getnumlen( stdin );
#endif
        rewind( stdin );

        seq = AllocateCharMtx( njob, nlenmax+1 );
        mtx = AllocateDoubleMtx( njob, njob );

#if 0
        FRead( stdin, name, nlen, seq );
#else
        readData( stdin, name, nlen, seq );
#endif

        for( i=0; i<njob-1; i++ ) 
        {
                fprintf( stderr, "%4d/%4d\r", i+1, njob );
                for( j=i+1; j<njob; j++ ) 
                        mtx[i][j] = (double)substitution_score( seq[i], seq[j] );
        }
        
#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 );
/*
        res = system( ALNDIR "/spgsdl < hat2"  );
        if( res ) exit( 1 );
        else exit( 0 );
*/
}