source: branches/lib/GDE/MAFFT/mafft-7.055-with-extensions/core/dndfast4.c

#include "mltaln.h"
#include <sys/types.h>
#include <unistd.h>
#define DEBUG 0
#define TEST 0


int howmanyx( char *s )
{
        int val = 0;
        if( scoremtx == -1 )
        {
                do
                {
                        if( !strchr( "atgcuATGCU", *s ) ) val++;
                } while( *++s );
        }
        else
        {
                do
                {
                        if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
                } while( *++s );
        }
        return( val );
}

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

        disopt = 0;

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

int main( int argc, char *argv[] )
{
        int ktuple;
        int i, j;
        FILE *hat2p;
        char **seq;
        char **seq1;
        static char name[M][B];
        static char name1[M][B];
        static int nlen1[M];
        double **mtx;
        double **mtx2;
        static int nlen[M];
        char b[B];
        double max;
        char com[B];
        int opt[M];
        int res;
        char *home;
        char queryfile[B];
        char datafile[B];
        char fastafile[B];
        char hat2file[B];
        int pid = (int)getpid();
#if 0
        home = getenv( "HOME" );
#else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */ 
        home = NULL;
#endif

#if DEBUG
        if( home ) fprintf( stderr, "home = %s\n", home );
#endif
        if( !home ) home = "";
        sprintf( queryfile, "%s/tmp/query-%d\0", home, pid );
        sprintf( datafile, "%s/tmp/data-%d\0", home, pid );
        sprintf( fastafile, "%s/tmp/fasta-%d\0", home, pid );
        sprintf( hat2file, "hat2-%d\0", pid );

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

        seq = AllocateCharMtx( njob, nlenmax+1 );
        seq1 = AllocateCharMtx( 2, nlenmax+1 );
        mtx = AllocateDoubleMtx( njob, njob );
        mtx2 = AllocateDoubleMtx( njob, njob );

#if 0
        FRead( stdin, name, nlen, seq );
#else
        readData( stdin, name, nlen, seq );
#endif
        if( scoremtx == -1 ) ktuple = 6;
        else                 ktuple = 1;

        for( i=0; i<njob; i++ )
        {
                gappick0( seq1[0], seq[i] ); 
                strcpy( seq[i], seq1[0] );
        }
        for( j=0; j<njob; j++ )
        {
                sprintf( name1[j], "+==========+%d                      \0", j );
                nlen1[j] = nlen[j];
        }
        hat2p = fopen( datafile, "w" );
        if( !hat2p ) ErrorExit( "Cannot open datafile." );
        WriteForFasta( hat2p, njob, name1, nlen1, seq );
        fclose( hat2p );

        for( i=0; i<njob; i++ ) 
        {

                hat2p = fopen( datafile, "w" );
                if( !hat2p ) ErrorExit( "Cannot open datafile." );
                WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
                fclose( hat2p );


                seq1[0] = seq[i];
                nlen1[0] = nlen[i];

                hat2p = fopen( queryfile, "w" );
                if( !hat2p ) ErrorExit( "Cannot open queryfile." );
                WriteForFasta( hat2p, 1, name1+i, nlen1, seq1 ); 
                fclose( hat2p );

                if( scoremtx == -1 )
                        sprintf( com, "fasta3 -n -Q -h -b%d -E%d -d%d %s %s %d > %s\0", M, M, 0, queryfile, datafile, ktuple, fastafile );
                else
                        sprintf( com, "fasta3 -Q -h -b%d -E%d -d%d %s %s %d > %s\0", M, M, 0, queryfile, datafile, ktuple, fastafile );
                res = system( com );
                if( res ) ErrorExit( "error in fasta" );

                hat2p = fopen( fastafile, "r" );
                if( hat2p == NULL ) 
                        ErrorExit( "file 'fasta.$$' does not exist\n" );
                ReadFasta3( hat2p, mtx[i], njob-i, name1 );

                if( i == 0 )
                        for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];

                fclose( hat2p );

#if 1
                {
                        int ii, jj;
                        if( i < njob-1 ) for( jj=i; jj<i+5; jj++ ) 
                                fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
                }
#endif
                fprintf( stderr, "query : %#4d\n", i+1 );
        }

        for( i=0; i<njob; i++ )
        {
                max = mtx[i][i];
                if( max == 0.0 )
                {
                        for( j=0; j<njob; j++ )
                                mtx2[i][j] = 2.0;
                }
                else
                {
                        for( j=0; j<njob; j++ )
                        {
                                mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
//                              fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
                        }
                }
        }
        for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
        {
//              fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
                mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
        }
#if 0
        {
                int ii, jj;
                if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ ) 
                        fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
        }
#endif

        for( i=0; i<njob; i++ ) name[i][0] = '=';

        if( disopt )
        {
                strcpy( b, name[0] );
                sprintf( name[0], "=query====lgth=%#04d-%04d %.*s\0", nlen[0], howmanyx( seq[0] ), B-30, b );
#if 0
                strins(  b, name[0] );
#endif
                for( i=1; i<njob; i++ ) 
                {       
                        strcpy( b, name[i] );
                        sprintf( name[i], "=opt=%#04d=lgth=%#04d-%04d %.*s\0", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
#if 0
                        strins( b, name[i] );
#endif
                }
        }

        hat2p = fopen( hat2file, "w" );
        if( !hat2p ) ErrorExit( "Cannot open hat2." );
        WriteHat2( hat2p, njob, name, mtx2 );
        fclose( hat2p );

        sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
        system( com );

#if 0
        sprintf( com, ALNDIR "/supgsdl < %s\0", hat2file );
        res = system( com );
        if( res ) ErrorExit( "error in spgsdl" );
#endif

        sprintf( com, "mv %s hat2", hat2file );
        res = system( com );
        if( res ) ErrorExit( "error in mv" );

        SHOWVERSION;
        exit( 0 );
}