/usr/lib/emboss/include/ajseqread.h is in emboss-lib 6.6.0+dfsg-6build1.
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 | /* @include ajseqread *********************************************************
**
** AJAX sequence reading functions
**
** These functions control all aspects of AJAX sequence reading
**
** @author Copyright (C) 2001 Peter Rice
** @version $Revision: 1.50 $
** @modified 2001-2011 pmr
** @modified $Date: 2011/10/18 14:23:40 $ 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 AJSEQREAD_H
#define AJSEQREAD_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajstr.h"
#include "ajlist.h"
#include "ajfile.h"
#include "ajseqdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
extern AjPTable seqDbMethods;
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
AjPTable ajSeqaccessGetDb(void);
AjBool ajSeqaccessMethodTest(const AjPStr method);
const char* ajSeqaccessMethodGetQlinks(const AjPStr method);
ajuint ajSeqaccessMethodGetScope(const AjPStr method);
AjPSeqall ajSeqallFile(const AjPStr usa);
AjBool ajSeqAllRead(AjPSeq thys, AjPSeqin seqin);
AjBool ajSeqGetFromUsa(const AjPStr thys, AjBool protein, AjPSeq seq);
AjBool ajSeqGetFromUsaRange(const AjPStr thys, AjBool protein,
ajint ibegin, ajint iend, AjPSeq seq);
AjBool ajSeqFormatTest(const AjPStr format);
void ajSeqinClear(AjPSeqin thys);
void ajSeqinClearPos(AjPSeqin thys);
void ajSeqinDel(AjPSeqin* pthis);
AjPSeqin ajSeqinNew(void);
AjPSeqin ajSeqinNewQueryC(const char* qrytxt);
AjPSeqin ajSeqinNewQueryS(const AjPStr qry);
void ajSeqinSetNuc(AjPSeqin seqin);
void ajSeqinSetProt(AjPSeqin seqin);
void ajSeqinSetRange(AjPSeqin seqin, ajint ibegin, ajint iend);
void ajSeqinUsa(AjPSeqin* pthis, const AjPStr Usa);
void ajSeqinTrace(const AjPSeqin thys);
const char* ajSeqinTypeGetFields(void);
const char* ajSeqinTypeGetQlinks(void);
AjBool ajSeqParseFasta(const AjPStr str, AjPStr* id, AjPStr* acc,
AjPStr* sv, AjPStr* desc);
AjBool ajSeqParseFastq(const AjPStr str, AjPStr* id, AjPStr* desc);
AjBool ajSeqParseNcbi(const AjPStr str, AjPStr* id, AjPStr* acc,
AjPStr* sv, AjPStr* gi, AjPStr* db, AjPStr* desc);
void ajSeqPrintInFormat(AjPFile outf, AjBool full);
void ajSeqPrintbookInFormat(AjPFile outf);
void ajSeqPrinthtmlInFormat(AjPFile outf);
void ajSeqPrintwikiInFormat(AjPFile outf);
AjBool ajSeqRead(AjPSeq thys, AjPSeqin seqin);
void ajSeqReadExit(void);
ajint ajSeqsetApp(AjPSeqset thys, const AjPSeq seq);
AjBool ajSeqsetGetFromUsa(const AjPStr thys, AjPSeqset *seq);
AjBool ajSeqsetFromList(AjPSeqset thys, const AjPList list);
ajint ajSeqsetFromPair(AjPSeqset thys,
const AjPSeq seqa, const AjPSeq seqb);
AjBool ajSeqsetallRead(AjPList thys, AjPSeqin seqin);
AjBool ajSeqsetRead(AjPSeqset thys, AjPSeqin seqin);
AjBool ajSeqUsaGetBase(const AjPStr usa, AjPStr* baseusa);
AjBool ajSeqinformatTerm(const AjPStr term);
AjBool ajSeqinformatTest(const AjPStr format);
/*
** End of prototype definitions
*/
#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */
#ifdef AJ_COMPILE_DEPRECATED
__deprecated AjBool ajSeqMethodTest(const AjPStr method);
__deprecated ajuint ajSeqMethodGetScope(const AjPStr method);
#endif /* AJ_COMPILE_DEPRECATED */
AJ_END_DECLS
#endif /* !AJSEQREAD_H */
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