/usr/include/genometools/core/translator_api.h is in libgenometools0-dev 1.5.1-2ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 | /*
Copyright (c) 2006-2008 Gordon Gremme <gremme@zbh.uni-hamburg.de>
Copyright (c) 2009 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
Copyright (c) 2006-2009 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 TRANSLATOR_API_H
#define TRANSLATOR_API_H
#include "core/codon_iterator_api.h"
#include "core/error_api.h"
#include "core/str_api.h"
#include "core/str_array_api.h"
#include "core/trans_table_api.h"
typedef enum {
GT_TRANSLATOR_OK = 0,
GT_TRANSLATOR_END = -1,
GT_TRANSLATOR_ERROR = -2
} GtTranslatorStatus;
/* The <GtTranslator> can be used to produce 3-frame translations of DNA
sequences via an iterator interface. */
typedef struct GtTranslator GtTranslator;
/* Creates a new <GtTranslator>, starting its translation at the current
position of <ci>. The current reading frame is also taken from the state of
<ci>. The translation table <tt> is used. */
GtTranslator* gt_translator_new_with_table(GtTransTable *tt,
GtCodonIterator *ci);
/* Creates a new <GtTranslator>, starting its translation at the current
position of <ci>. The current reading frame is also taken from the state of
<ci>. The standard translation table is used. */
GtTranslator* gt_translator_new(GtCodonIterator *ci);
/* Reinitializes <translator> with the position and frame status as given in
<ci>. */
void gt_translator_set_codon_iterator(GtTranslator *translator,
GtCodonIterator *ci);
/* Selects the translation scheme in <translator> to the one identified by
translation table <tt>. */
void gt_translator_set_translation_table(GtTranslator *translator,
GtTransTable *tt);
/* Returns the translation of the next codon. The currently translated
character is put in <translated> while the current reading frame is put in
<frame>.
Returns GT_TRANSLATOR_ERROR if an error occurred, see <err> for details.
If the end of the sequence region to translate has been reached,
GT_TRANSLATOR_END is returned.
Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned. */
GtTranslatorStatus gt_translator_next(GtTranslator *translator,
char *translated,
unsigned int *frame,
GtError *err);
/* Moves the <translator> to the beginning of the first codon in <dnaseq> (of
length <dnalen>) which is a start codon according to the selected translation
scheme in <translator>.
The offset is written to the location pointed to by <pos>.
Returns GT_TRANSLATOR_ERROR if an error occurred, see <err> for details.
If the end of the sequence region to scan has been reached without finding a
start codon, GT_TRANSLATOR_END is returned.
Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned. */
GtTranslatorStatus gt_translator_find_startcodon(GtTranslator *translator,
unsigned long *pos,
GtError *err);
/* Moves the <translator> to the beginning of the first codon in <dnaseq> (of
length <dnalen>) which is a stop codon according to the selected translation
scheme in <translator>.
The offset is written to the location pointed to by <pos>.
Returns GT_TRANSLATOR_ERROR if an error occurred, see <err> for details.
If the end of the sequence region to scan has been reached without finding a
stop codon, GT_TRANSLATOR_END is returned.
Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned. */
GtTranslatorStatus gt_translator_find_stopcodon(GtTranslator *translator,
unsigned long *pos,
GtError *err);
/* Moves the <translator> to the beginning of the first codon in <dnaseq> (of
length <dnalen>) which belongs to the set of codons specified in <codons>.
The offset is written to the location pointed to by <pos>.
Returns GT_TRANSLATOR_ERROR if an error occurred, see <err> for details.
If the end of the sequence region to scan has been reached without finding
one of the codons, GT_TRANSLATOR_END is returned.
Otherwise, GT_TRANSLATOR_OK (equal to 0) is returned. */
GtTranslatorStatus gt_translator_find_codon(GtTranslator *translator,
GtStrArray *codons,
unsigned long *pos,
GtError *err);
/* Delete <translator>. */
void gt_translator_delete(GtTranslator *translator);
#endif
|