source: branches/items/GDE/MAFFT/mafft-7.055-with-extensions/core/regtable2seq.c

#include "mltaln.h"

#define DEBUG 0

char *regfile;
char *eregfile;

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

    outnumber = 0;
    inputfile = NULL;
    regfile = NULL;
    eregfile = NULL;

    while( --argc > 0 && (*++argv)[0] == '-' )
        {
        while ( (c = *++argv[0]) )
                {
            switch( c )
            {
                                case 'e':
                                        eregfile = *++argv;
                                        fprintf( stderr, "eregfile = %s\n", eregfile );
                                        --argc;
                                        goto nextoption;
                                case 'r':
                                        regfile = *++argv;
                                        fprintf( stderr, "regfile = %s\n", regfile );
                                        --argc;
                                        goto nextoption;
                                case 'i':
                                        inputfile = *++argv;
                                        fprintf( stderr, "inputfile = %s\n", inputfile );
                                        --argc;
                                        goto nextoption;
                                case 'n' :
                                        outnumber = 1;
                                        break;
                default:
                    fprintf( stderr, "illegal option %c\n", c );
                    argc = 0;
                    break;
            }
                }
                nextoption:
                        ;
        }
    if( argc != 0 ) 
    {
        fprintf( stderr, "options: Check source file !\n" );
        exit( 1 );
    }
}

void readereg( FILE *regfp, int **regtable, char **revtable, int *outtable, int *noutpt, int *loutpt )
{
        char gett[1000];
        int j;
        int mem;
        char cmem;
        char reg[5][100];
        char out[100];
        int startpos, endpos;

        *noutpt = 0;
        *loutpt = 0;
        fgets( gett, 999, regfp );
        sscanf( gett, "%c %s %s %s %s %s", &cmem, reg[0], reg[1], reg[2], reg[3], reg[4] );
        if( cmem != 'e' )
        {
                fprintf( stderr, "Format error\n" );
                exit( 1 );
        }
        for( j=0; j<5; j++ )
        {
                sscanf( reg[j], "%d-%d-%c", regtable[0]+(j*2), regtable[0]+(j*2)+1, revtable[0]+j );
                fprintf( stderr, "%d %d-%d\n", 0, regtable[0][j*2], regtable[0][j*2+1] );
                startpos = regtable[0][j*2];
                endpos   = regtable[0][j*2+1];
                if( startpos > endpos )
                {
                        endpos   = regtable[0][j*2];
                        startpos = regtable[0][j*2+1];
                }
                if( startpos != -1 && endpos != -1 )
                        *loutpt += endpos - startpos + 1;
        }

        while( 1 )
        {
                fgets( gett, 999, regfp );
                if( feof( regfp ) ) break;
                sscanf( gett, "%d o=%s", &mem, out );
                if( mem >= njob )
                {
                        fprintf( stderr, "Out of range\n" );
                        exit( 1 );
                }
                outtable[mem] = atoi( out );
                if( outtable[mem] ) *noutpt += 1;
        }
}

void readreg( FILE *regfp, int **regtable, char **revtable, int *outtable )
{
        char gett[1000];
        int j;
        int mem;
        char reg[5][100];
        char out[100];

        while( 1 )
        {
                fgets( gett, 999, regfp );
                if( feof( regfp ) ) break;
                sscanf( gett, "%d %s %s %s %s %s o=%s", &mem, reg[0], reg[1], reg[2], reg[3], reg[4], out );
                if( mem >= njob )
                {
                        fprintf( stderr, "Out of range\n" );
                        exit( 1 );
                }
                for( j=0; j<5; j++ )
                {
                        sscanf( reg[j], "%d-%d-%c", regtable[mem]+(j*2), regtable[mem]+(j*2)+1, revtable[mem]+j );
                        fprintf( stderr, "%d %d-%d\n", mem, regtable[mem][j*2], regtable[mem][j*2+1] );
                }
                outtable[mem] = atoi( out );
        }
}

int main( int argc, char *argv[] )
{
        FILE *infp;
        FILE *regfp;
        int nlenmin;
        int **regtable;
        char **revtable;
        int *outtable;
        int i, nout, lout;
        char **outseq;
        char **name;

        arguments( argc, argv );

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

        dorp = NOTSPECIFIED;
        getnumlen_nogap( infp, &nlenmin );

        if( regfile )
        {
                regfp = fopen( regfile, "r" );
                if( !regfp )
                {
                        fprintf( stderr, "Cannot open %s\n", regfile );
                        exit( 1 );
                }
                regtable = AllocateIntMtx( njob, 5*2 );
                revtable = AllocateCharMtx( njob, 5 );
                outtable = AllocateIntVec( njob );
                readreg( regfp, regtable, revtable, outtable );
                cutData( infp, regtable, revtable, outtable );
        }
        else if( eregfile )
        {
                regfp = fopen( eregfile, "r" );
                if( !regfp )
                {
                        fprintf( stderr, "Cannot open %s\n", eregfile );
                        exit( 1 );
                }
                regtable = AllocateIntMtx( 1, 5*2 );
                revtable = AllocateCharMtx( 1, 5 );
                outtable = AllocateIntVec( njob );
                readereg( regfp, regtable, revtable, outtable, &nout, &lout );
                fprintf( stderr, "nout = %d, lout = %d\n", nout, lout );

                outseq = AllocateCharMtx( nout, lout+1 );
                name = AllocateCharMtx( nout, B );

                cutAlignment( infp, regtable, revtable, outtable, name, outseq );
                fprintf( stderr, "gappick! nout = %d\n", nout );
                commongappick( nout, outseq );
                for( i=0; i<nout; i++ )
                {
                        fprintf( stdout, "%s\n", name[i] );
                        fprintf( stdout, "%s\n", outseq[i] );
                }
        }
        else
        {
                catData( infp );
        }

        fprintf( stderr, "Strategy:\n" );
        fprintf( stderr, " Not-Aligned\n" );

//      fprintf( stdout, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
        return( 0 );
}