/usr/include/genometools/extended/match_blast_api.h is in libgenometools0-dev 1.5.9+ds-4.
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 | /*
Copyright (c) 2011 Sascha Kastens <mail@skastens.de>
Copyright (c) 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 MATCH_BLAST_API_H
#define MATCH_BLAST_API_H
typedef struct GtMatchBlast GtMatchBlast;
#include "extended/match_api.h"
/* Creates a new <GtMatch> object meant to store results in the BLAST
format. That is, it stores double values <evalue> for match E-values,
<bitscore>s and the alignment length <ali_l> in addition to the generic
match contents <seqid1>, <seqid2>, <start_seq1>, <start_seq2>, <end_seq1>,
and <end_seq2>. */
GtMatch* gt_match_blast_new(char *seqid1,
char *seqid2,
GtUword start_seq1,
GtUword start_seq2,
GtUword end_seq1,
GtUword end_seq2,
double evalue,
float bitscore,
GtUword ali_l,
double similarity,
GtMatchDirection dir);
/* Sets <evalue> to be the E-value in <mb>. */
void gt_match_blast_set_evalue(GtMatchBlast *mb, double evalue);
/* Sets <bits> to be the bit-score in <mb>. */
void gt_match_blast_set_bitscore(GtMatchBlast *mb, float bits);
/* Sets <length> to be the alignment length in <mb>. */
void gt_match_blast_set_align_length(GtMatchBlast *mb, GtUword length);
/* Sets <similarity> to be the match similarity in <mb>. */
void gt_match_blast_set_similarity(GtMatchBlast *mb, double similarity);
/* Returns the E-value stored in <mb>. */
double gt_match_blast_get_evalue(GtMatchBlast *mb);
/* Returns the bit-score value stored in <mb>. */
float gt_match_blast_get_bitscore(GtMatchBlast *mb);
/* Returns the alignment length stored in <mb>. */
GtUword gt_match_blast_get_align_length(GtMatchBlast *mb);
/* Returns the alignment similarity stored in <mb>. */
double gt_match_blast_get_similarity(GtMatchBlast *mb);
#endif
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