fasta.c

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/*
 * Copyright (c) 2007-2008 ETH Zürich, Institute of Computational Science
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

#include "fasta.h"
#include "swps3.h"
#include "debug.h"
#include <stdlib.h>
#ifdef HAVE_MALLOC_H
#include <malloc.h>
#endif /* HAVE_MALLOC_H */
#include <string.h>
#include <errno.h>

EXPORT FastaLib * swps3_openLib( char * filename ){
        FastaLib * lib = NULL;
        FILE * fp;
        int len;
        if ( (fp = fopen( filename, "r" )) ){
#ifdef HAVE_MALLOC_H
                lib = memalign( 16, sizeof( FastaLib ) );
#else
                lib = malloc( sizeof( FastaLib ) );
#endif /* HAVE_MALLOC_H */
                lib->fp = fp;
                lib->name = "";
        }
        else{
                error("Fasta: %s\n",strerror(errno));
        }
        swps3_readNextSequence( lib, &len );
        if (len)
                rewind( lib->fp );
        return lib;
}
EXPORT char * swps3_readNextSequence( FastaLib * lib, int * len ){
        char * pres = lib->readBuffer;
        if ( feof( lib->fp ) )
                return NULL;
        if( (*pres = fgetc(lib->fp)) != '>' ) {
           warning("Missing comment line, trying to continue anyway\n");
           lib->name = "";
           lib->data = pres++;
           goto readseq;
        } else {
           fgets( pres, sizeof(lib->readBuffer)-(pres-lib->readBuffer), lib->fp );
           lib->name = pres;
           for (;*pres && *pres!='\n';pres++);
           *pres++ = '\0';
           while ((long)pres&0xf) *pres++ = '\0';
           lib->data = pres;
        }
        while ( (*pres = fgetc( lib->fp) ) != '>' ){
readseq:
                if( fgets( pres+1, sizeof(lib->readBuffer)-(pres+1-lib->readBuffer), lib->fp ) == 0 ) goto finish;
                for (;*pres && *pres!='\n';pres++)
                        if ('A'>*pres || *pres>'Z'){
                                error("Invalid character in input sequence '%c'\n", *pres);
                        }
        }
        *pres = '\0';
        ungetc( '>', lib->fp );
finish:
        if (len)
                *len = pres - lib->data;
        swps3_translateSequence(lib->data,pres - lib->data,NULL);
        return lib->data;
}
EXPORT char * swps3_getSequenceName( FastaLib * lib ){
        return lib->name;
}
EXPORT void swps3_closeLib( FastaLib * lib ){
        free( lib );
}
EXPORT void swps3_translateSequence(char *sequence, int seqLen, char table[256]) {
   int i;
   for(i=0;i<seqLen && sequence[i]!='\n' && sequence[i]!='\0';++i) {
      if(table) sequence[i] = table[(int)sequence[i]];
      else sequence[i] -= 'A';

      if(sequence[i] < 0 || sequence[i] >= MATRIX_DIM) error("Invalid character in input sequence at position %d\n",i);
   }
}

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