/usr/lib/emboss/include/embdmx.h is in emboss-lib 6.6.0+dfsg-1.
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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 | /* @include embdmx ************************************************************
**
** Algorithms for some of the DOMAINATRIX EMBASSY applications.
** For use with the Scophit and Scopalign objects.
** The functionality will eventually be subsumed by other AJAX and NUCLEUS
** libraries.
**
** @author Copyright (C) 2004 Ranjeeva Ranasinghe (rranasin@hgmp.mrc.ac.uk)
** @author Copyright (C) 2004 Jon Ison (jison@hgmp.mrc.ac.uk)
** @version $Revision: 1.20 $
** @modified $Date: 2011/10/18 14:24:24 $ by $Author: rice $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
****************************************************************************/
#ifndef EMBDMX_H
#define EMBDMX_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajlist.h"
#include "ajfile.h"
#include "ajseqdata.h"
#include "ajdmx.h"
#include "ajarr.h"
#include "ajmatrices.h"
#include "embsig.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @data EmbPDmxNrseq *********************************************************
**
** NUCLEUS data structure for non-redundant sequence testing
**
** @attr Seq [AjPSeq] Sequence to be tested for redundancy
** @attr Garbage [AjBool] True if sequence is to be ignored
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EmbSDmxNrseq {
AjPSeq Seq;
AjBool Garbage;
char Padding[4];
} EmbODmxNrseq;
#define EmbPDmxNrseq EmbODmxNrseq*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
void embDmxNrseqDel(EmbPDmxNrseq* Pnrseq);
EmbPDmxNrseq embDmxNrseqNew(const AjPSeq seq);
AjPList embDmxScophitReadAllFasta(AjPFile in);
AjBool embDmxHitlistToScophits(const AjPList in,
AjPList out);
AjBool embDmxScophitsToHitlist(const AjPList in,
EmbPHitlist *out,
AjIList *iter);
AjBool embDmxScophitToHit(EmbPHit *to,
const AjPScophit from);
AjBool embDmxScophitsAccToHitlist(const AjPList in,
EmbPHitlist *out,
AjIList *iter);
AjBool embDmxHitsWrite(AjPFile outf,
EmbPHitlist hits,
ajint maxhits);
AjBool embDmxScopToScophit(const AjPScop source,
AjPScophit* target);
AjBool embDmxScopalgToScop(const AjPScopalg align,
AjPScop const *scop_arr,
ajint scop_dim,
AjPList* list);
AjBool embDmxScophitsOverlap(const AjPScophit h1,
const AjPScophit h2,
ajuint n);
AjBool embDmxScophitsOverlapAcc(const AjPScophit h1,
const AjPScophit h2,
ajuint n);
AjPScophit embDmxScophitMerge(const AjPScophit hit1,
const AjPScophit hit2);
AjBool embDmxScophitMergeInsertThis(const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter);
AjBool embDmxScophitMergeInsertThisTarget(const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter);
AjBool embDmxScophitMergeInsertThisTargetBoth(const AjPList list,
AjPScophit hit1,
AjPScophit hit2,
AjIList iter);
AjBool embDmxScophitMergeInsertOther(AjPList list,
AjPScophit hit1,
AjPScophit hit2);
AjBool embDmxScophitMergeInsertOtherTargetBoth(AjPList list,
AjPScophit hit1,
AjPScophit hit2);
AjBool embDmxScophitMergeInsertOtherTarget(AjPList list,
AjPScophit hit1,
AjPScophit hit2);
AjBool embDmxSeqNR(const AjPList input,
AjPUint *keep,
ajint *nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh,
AjBool CheckGarbage);
AjBool embDmxSeqNRRange(const AjPList input,
AjPUint *keep,
ajint *nset,
const AjPMatrixf matrix,
float gapopen,
float gapextend,
float thresh1,
float thresh2,
AjBool CheckGarbage);
AjBool embDmxSeqCompall(const AjPList input,
AjPFloat2d *scores,
const AjPMatrixf matrix,
float gapopen,
float gapextend);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !EMBDMX_H */
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