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

#include "mltaln.h"

#define DEBUG 0

char *directionfile;

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

        inputfile = NULL;
        directionfile = NULL;

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



int main( int argc, char *argv[] )
{
        FILE *infp;
        FILE *difp;
        int nlenmin;
        char **name;
        char **seq;
        char *tmpseq;
        char line[100];
        int *nlen;
        int i;

        arguments( argc, argv );

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

        if( directionfile )
        {
                difp = fopen( directionfile, "r" );
                if( !difp )
                {
                        fprintf( stderr, "Cannot open %s\n", directionfile );
                        exit( 1 );
                }
        }
        else
        {
                fprintf( stderr, "Give directionfile!\n" );
        }


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

        fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );

        seq = AllocateCharMtx( njob, nlenmax+1 );
        tmpseq = AllocateCharVec( MAX( B, nlenmax )+1 );
        name = AllocateCharMtx( njob, B+1 );
        nlen = AllocateIntVec( njob );

        readData_pointer_casepreserve( infp, name, nlen, seq );

        for( i=0; i<njob; i++ )
        {
                fgets( line, 99, difp );
                if( line[0] != '_' )
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
                if( line[1] == 'R' )
                {
                        sreverse( tmpseq, seq[i] );
                        strcpy( seq[i], tmpseq );

                        strncpy( tmpseq, name[i]+1, B-3 );
                        tmpseq[B-3] = 0;
                        strcpy( name[i]+1, "_R_" );
                        strcpy( name[i]+4, tmpseq );
                }
                else if( line[1] == 'F' )
                {
                        ;
                }
                else
                {
                        fprintf( stderr, "Format error!\n" );
                        exit( 1 );
                }
        }


        for( i=0; i<njob; i++ )
        {
                fprintf( stdout, ">%s\n", name[i]+1 );
                fprintf( stdout, "%s\n", seq[i] );
        }

        free( nlen );
        FreeCharMtx( seq );
        FreeCharMtx( name );
        free( tmpseq );

        return( 0 );
}