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

#include "mltaln.h"

#define DEBUG 0

static int seedoffset;

static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
{
        int i;
        char *pt;
        for( i=0; i<n; i++ )
        {
                pt = seq[i];
                while( *pt )
                {
                        if( !strchr( usual, *pt ) ) *pt = unknown;
                        else *pt = uporlow( *pt );
                        pt++;
                }
        }
}


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

        seedoffset = 0;
        inputfile = NULL;

    while( --argc > 0 && (*++argv)[0] == '-' )
        {
        while ( (c = *++argv[0]) )
                {
            switch( c )
            {
                                case 'o':
                                        seedoffset = atoi( *++argv );
                                        fprintf( stderr, "seedoffset = %d\n", seedoffset );
                                        --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;
        int nlenmin;
        char **name;
        char **seq;
        int *nlen;
        int i;
        char *usual;

        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_casepreserve( infp, &nlenmin );

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

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

        readData_pointer_casepreserve( infp, name, nlen, seq );

//      for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );

#if 0
        FILE *origfp;
        origfp = fopen( "_original", "w" );
        if( !origfp )
        {
                fprintf( stderr, "Cannot open _original\n" );
                exit( 1 );
        }
        for( i=0; i<njob; i++ )
        {
                nlen[i] = strlen( seq[i] );
                fprintf( origfp, ">%s\n", name[i]+1 );
                if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
                fprintf( origfp, "%s\n", seq[i] );
        }
        fclose( origfp );
#endif

        if( dorp == 'p' )
        {
                usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
                replace_unusual( njob, seq, usual, 'X', toupper );
        }
        else
        {
                usual = "ATGCUatgcuBDHKMNRSVWYXbdhkmnrsvwyx-";
                replace_unusual( njob, seq, usual, 'n', tolower );
        }
        


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

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

        return( 0 );
}