/usr/include/genometools/extended/sequence_node_api.h is in libgenometools0-dev 1.5.8-2.
This file is owned by root:root, with mode 0o644.
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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 | /*
Copyright (c) 2008 Gordon Gremme <gordon@gremme.org>
Copyright (c) 2008 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 SEQUENCE_NODE_API_H
#define SEQUENCE_NODE_API_H
/* Implements the <GtGenomeNode> interface. Sequence nodes correspond to
singular embedded FASTA sequences in GFF3 files. */
typedef struct GtSequenceNode GtSequenceNode;
#include "core/str_api.h"
#include "extended/genome_node_api.h"
const GtGenomeNodeClass* gt_sequence_node_class(void);
/* Create a new <GtSequenceNode*> representing a FASTA entry with the given
<description> and <sequence>. Takes ownership of <sequence>. */
GtGenomeNode* gt_sequence_node_new(const char *description,
GtStr *sequence);
/* Return the description of <sequence_node>. */
const char* gt_sequence_node_get_description(const
GtSequenceNode
*sequence_node);
/* Return the sequence of <sequence_node>. */
const char* gt_sequence_node_get_sequence(const GtSequenceNode
*sequence_node);
/* Return the sequence length of <sequence_node>. */
GtUword gt_sequence_node_get_sequence_length(const
GtSequenceNode
*sequence_node);
/* Test whether the given genome node is a sequence node. If so, a pointer to
the sequence node is returned. If not, NULL is returned. Note that in most
cases, one should implement a GtNodeVisitor to handle processing of different
GtGenomeNode types. */
GtSequenceNode* gt_sequence_node_try_cast(GtGenomeNode *gn);
/* Test whether the given genome node is a sequence node. If so, a pointer to
the sequence node is returned. If not, an assertion fails. */
GtSequenceNode* gt_sequence_node_cast(GtGenomeNode *gn);
#endif
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