source: branches/items/GDE/MAFFT/mafft-7.055-with-extensions/core/sextet5.c

#include "mltaln.h"
#include "mtxutl.h"

#define DEBUG 0
#define TEST  0

#define END_OF_VEC -1

static int maxl;
static int tsize;

void arguments( int argc, char *argv[] )
{
        int c;

        inputfile = NULL;
        disopt = 0;
        scoremtx = 1;
        nblosum = 62;
        dorp = NOTSPECIFIED;

    while( --argc > 0 && (*++argv)[0] == '-' )
        {
        while ( ( c = *++argv[0] ) )
                {
            switch( c )
            {
                                case 'i':
                                        inputfile = *++argv;
                                        fprintf( stderr, "inputfile = %s\n", inputfile );
                                        --argc;
                                        goto nextoption;
                                case 'D':
                                        dorp = 'd';
                                        break;
                                case 'P':
                                        dorp = 'p';
                                        break;
                                case 'I':
                                        disopt = 1;
                                        break;
                default:
                    fprintf( stderr, "illegal option %c\n", c );
                    argc = 0;
                    break;
            }
                }
                nextoption:
                        ;
        }
    if( argc != 0 )
    {
        fprintf( stderr, "options: -i\n" );
        exit( 1 );
    }
}

void seq_grp_nuc( int *grp, char *seq )
{
        int tmp;
        while( *seq )
        {
                tmp = amino_grp[(int)*seq++];
                if( tmp < 4 )
                        *grp++ = tmp;
                else
                        fprintf( stderr, "WARNING : Unknown character %c\n", *(seq-1) );
        }
        *grp = END_OF_VEC;
}

void seq_grp( int *grp, char *seq )
{
        int tmp;
        while( *seq )
        {
                tmp = amino_grp[(int)*seq++];
                if( tmp < 6 )
                        *grp++ = tmp;
                else
                        fprintf( stderr, "WARNING : Unknown character %c\n", *(seq-1) );
        }
        *grp = END_OF_VEC;
}

void makecompositiontable_p( short *table, int *pointt )
{
        int point;

        while( ( point = *pointt++ ) != END_OF_VEC )
                table[point]++;
}

int commonsextet_p( short *table, int *pointt )
{
        int value = 0;
        short tmp;
        int point;
        static short *memo = NULL;
        static int *ct = NULL;
        static int *cp;

        if( !memo )
        {
                memo = (short *)calloc( tsize, sizeof( short ) );
                if( !memo ) ErrorExit( "Cannot allocate memo\n" );
                ct = (int *)calloc( MIN( maxl, tsize)+1, sizeof( int ) );
                if( !ct ) ErrorExit( "Cannot allocate memo\n" );
        }

        cp = ct;
        while( ( point = *pointt++ ) != END_OF_VEC )
        {
                tmp = memo[point]++;
                if( tmp < table[point] )
                        value++;
                if( tmp == 0 ) *cp++ = point;
//              fprintf( stderr, "cp - ct = %d (tsize = %d)\n", cp - ct, tsize );
        }
        *cp = END_OF_VEC;
        
        cp =  ct;
        while( *cp != END_OF_VEC )
                memo[*cp++] = 0;

        return( value );
}

void makepointtable_nuc( int *pointt, int *n )
{
        int point;
        register int *p;

        p = n;
        point  = *n++ *  1024;
        point += *n++ *   256;
        point += *n++ *    64;
        point += *n++ *    16;
        point += *n++ *     4;
        point += *n++;
        *pointt++ = point;

        while( *n != END_OF_VEC )
        {
                point -= *p++ * 1024;
                point *= 4;
                point += *n++;
                *pointt++ = point;
        }
        *pointt = END_OF_VEC;
}

void makepointtable( int *pointt, int *n )
{
        int point;
        register int *p;

        p = n;
        point  = *n++ *  7776;
        point += *n++ *  1296;
        point += *n++ *   216;
        point += *n++ *    36;
        point += *n++ *     6;
        point += *n++;
        *pointt++ = point;

        while( *n != END_OF_VEC )
        {
                point -= *p++ * 7776;
                point *= 6;
                point += *n++;
                *pointt++ = point;
        }
        *pointt = END_OF_VEC;
}

int main( int argc, char **argv )
{
        int i, j;
        FILE *fp, *infp;
        char **seq;
        int *grpseq;
        char *tmpseq;
        int  **pointt;
        static char **name;
        static int nlen[M];
        double **mtx;
        double **mtx2;
        double score, score0;
        static short *table1;
        char b[B];

        arguments( argc, argv );

        if( inputfile )
        {
                infp = fopen( inputfile, "r" );
                if( !infp )
                {
                        fprintf( stderr, "Cannot open %s\n", inputfile );
                        exit( 1 );
                }
        }
        else
                infp = stdin;

#if 0
        PreRead( stdin, &njob, &nlenmax );
#else
        getnumlen( infp );
#endif
        rewind( infp );
        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 );
        tmpseq = AllocateCharVec( nlenmax+1 );
        seq = AllocateCharMtx( njob, nlenmax+1 );
        grpseq = AllocateIntVec( nlenmax+1 );
        pointt = AllocateIntMtx( njob, nlenmax+1 );
        mtx = AllocateDoubleMtx( njob, njob );
        mtx2 = AllocateDoubleMtx( njob, njob );
        pamN = NOTSPECIFIED;

#if 0
        FRead( infp, name, nlen, seq );
#else
        readData_pointer( infp, name, nlen, seq );
#endif

        fclose( infp );

        constants( njob, seq );

        if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
        else              tsize = (int)pow( 6, 6 );

        maxl = 0;
        for( i=0; i<njob; i++ ) 
        {
                gappick0( tmpseq, seq[i] );
                nlen[i] = strlen( tmpseq );
                if( nlen[i] < 6 )
                {
                        fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
                        exit( 1 );
                }
                if( nlen[i] > maxl ) maxl = nlen[i];
                if( dorp == 'd' ) /* nuc */
                {
                        seq_grp_nuc( grpseq, tmpseq );
                        makepointtable_nuc( pointt[i], grpseq );
                }
                else                 /* amino */
                {
                        seq_grp( grpseq, tmpseq );
                        makepointtable( pointt[i], grpseq );
                }
        }
        for( i=0; i<njob; i++ )
        {
                table1 = (short *)calloc( tsize, sizeof( short ) );
                if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
                if( i % 10 == 0 )
                {
                        fprintf( stderr, "%4d / %4d\r", i+1, njob );
                }
                makecompositiontable_p( table1, pointt[i] );

                for( j=i; j<njob; j++ ) 
                {
                        score = (double)commonsextet_p( table1, pointt[j] );
                        mtx[i][j] = score;
                } 
                free( table1 );
        }
        for( i=0; i<njob; i++ )
        {
                score0 = mtx[i][i];
                for( j=0; j<njob; j++ ) 
                        mtx2[i][j] = ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3.0;
        }
        for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) 
        {
#if TEST
                double jscore;
                jscore = mtx[i][j] / ( MIN( strlen( seq[i] ), strlen( seq[j] ) ) - 2 );
                fprintf( stdout, "jscore = %f\n", jscore );

                fprintf( stdout, "mtx2[%d][%d] = %f, mtx2[%d][%d] = %f\n", i, j, mtx2[i][j], j, i, mtx2[j][i] );
#endif
                mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
#if TEST
                fprintf( stdout, "sonokekka mtx2[%d][%d] %f\n", i, j, mtx2[i][j] );
#endif
        }

        if( disopt )
        {
                for( i=0; i<njob; i++ ) 
                {
                        sprintf( b, "=lgth = %04d", nlen[i] );
                        strins( b, name[i] );
                }
        }
                
        fp = fopen( "hat2", "w" );
        if( !fp ) ErrorExit( "Cannot open hat2." );
        WriteHat2_pointer( fp, njob, name, mtx2 );
        fclose( fp );

        fprintf( stderr, "\n" );
        SHOWVERSION;
        exit( 0 );
}