/usr/include/genometools/extended/orf_iterator_api.h is in libgenometools0-dev 1.5.10+ds-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | /*
Copyright (c) 2010 Sascha Kastens <mail@skastens.de>
Copyright (c) 2011 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef ORF_ITERATOR_API_H
#define ORF_ITERATOR_API_H
#include "core/codon_iterator_api.h"
#include "core/translator_api.h"
#include "core/range_api.h"
#include "core/error_api.h"
typedef enum {
GT_ORF_ITERATOR_OK = 0,
GT_ORF_ITERATOR_END = -1,
GT_ORF_ITERATOR_ERROR = -2
} GtORFIteratorStatus;
/* The <GtORFIterator> class is used to enumerate open reading frames (ORFs)
in codon streams as delivered by a <GtCodonIterator> using a translation
process as defined by a <GtTranslator>. */
typedef struct GtORFIterator GtORFIterator;
/* Return a new <GtORFIterator*> using the codons delivered by <ci> and
translated by <translator>. */
GtORFIterator* gt_orf_iterator_new(GtCodonIterator *ci,
GtTranslator *translator);
/* Sets the values of <orf_rng.start>, <orf_rng.end> and <orf_frame> to the
current reading position of <ci> if a START/STOP codon is found. The frame
in which the ORF is located is written to the position pointed to by
<orf_frame>. This function returns one of three status codes:
<GT_ORF_ITERATOR_OK> if an ORF was detected successfully(START/STOP AA pair),
<GT_ORF_ITERATOR_END> if no ORF was detected because the end of the scan
region has been reached, or
<GT_ORF_ITERATOR_ERROR> if no ORF was detected because an error occurred
during sequence access. See <err> for details. */
GtORFIteratorStatus gt_orf_iterator_next(GtORFIterator *orf_iterator,
GtRange *orf_rng,
unsigned int *orf_frame,
GtError *err);
/* Delete <orf_iterator> and frees all associated memory. */
void gt_orf_iterator_delete(GtORFIterator *orf_iterator);
#endif
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