/usr/lib/emboss/include/ajseqwrite.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 | /* @include ajseqwrite ********************************************************
**
** AJAX seqwrite functions
**
** @author Copyright (C) 2001 Peter Rice
** @version $Revision: 1.52 $
** @modified 2001-2011 Peter Rice
** @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 AJSEQWRITE_H
#define AJSEQWRITE_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajstr.h"
#include "ajfile.h"
#include "ajseqdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
AjBool ajSeqoutWriteSeq(AjPSeqout outseq, const AjPSeq seq);
AjBool ajSeqoutOpenFilename(AjPSeqout seqout, const AjPStr name);
ajint ajSeqoutGetCheckgcg(const AjPSeqout outseq);
const AjPStr ajSeqoutGetFilename(const AjPSeqout thys);
void ajSeqoutClear(AjPSeqout thys);
void ajSeqoutGetBasecount(const AjPSeqout seqout, ajuint* bases);
AjBool ajSeqoutSetNameDefaultC(AjPSeqout thys,
AjBool multi, const char* txt);
AjBool ajSeqoutSetNameDefaultS(AjPSeqout thys,
AjBool multi, const AjPStr str);
void ajSeqoutDel(AjPSeqout* thys);
AjBool ajSeqoutstrGetFormatDefault(AjPStr* Pformat);
AjBool ajSeqoutstrIsFormatExists(const AjPStr format);
AjBool ajSeqoutstrIsFormatSingle(const AjPStr format);
AjPSeqout ajSeqoutNew(void);
AjPSeqout ajSeqoutNewFile(AjPFile file);
AjPSeqout ajSeqoutNewFormatC(const char* txt);
AjPSeqout ajSeqoutNewFormatS(const AjPStr str);
AjBool ajSeqoutOpen(AjPSeqout thys);
AjBool ajSeqoutSetFormatC(AjPSeqout thys, const char* format);
AjBool ajSeqoutSetFormatS(AjPSeqout thys, const AjPStr format);
void ajSeqoutTrace(const AjPSeqout seq);
void ajSeqoutPrintFormat(AjPFile outf, AjBool full);
void ajSeqoutPrintbookFormat(AjPFile outf);
void ajSeqoutPrinthtmlFormat(AjPFile outf);
void ajSeqoutPrintwikiFormat(AjPFile outf);
void ajSeqoutClearUsa(AjPSeqout thys, const AjPStr Usa);
AjBool ajSeqoutWriteSet(AjPSeqout seqout, const AjPSeqset seq);
void ajSeqoutClose(AjPSeqout outseq);
void ajSeqoutCloseEmpty(AjPSeqout outseq);
void ajSeqoutFlush(AjPSeqout seqout);
void ajSeqoutExit(void);
void ajSeqoutReset(AjPSeqout seqout);
void ajSeqoutDumpSwisslike(AjPSeqout outseq,const AjPStr seq,
const char *prefix);
/*
** End of prototype definitions
*/
#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */
#ifdef AJ_COMPILE_DEPRECATED
__deprecated void ajSeqoutCount(const AjPSeqout seqout, ajuint* b);
__deprecated void ajSeqAllWrite(AjPSeqout outseq, const AjPSeq seq);
__deprecated AjBool ajSeqFileNewOut(AjPSeqout seqout,
const AjPStr name);
__deprecated AjPSeqout ajSeqoutNewF(AjPFile file);
__deprecated void ajSeqWrite(AjPSeqout seqout, const AjPSeq seq);
__deprecated void ajSeqsetWrite(AjPSeqout outseq, const AjPSeqset seq);
__deprecated void ajSeqWriteClose(AjPSeqout outseq);
__deprecated AjBool ajSeqOutFormatSingle(AjPStr format);
__deprecated AjBool ajSeqOutSetFormat(AjPSeqout thys,
const AjPStr format);
__deprecated AjBool ajSeqOutSetFormatC(AjPSeqout thys,
const char* format);
__deprecated AjBool ajSeqOutFormatDefault(AjPStr* pformat);
__deprecated void ajSeqoutUsa(AjPSeqout* pthis, const AjPStr Usa);
__deprecated void ajSeqPrintOutFormat(AjPFile outf, AjBool full);
__deprecated AjBool ajSeqFindOutFormat(const AjPStr format,
ajint* iformat);
__deprecated void ajSeqWriteExit(void);
__deprecated ajint ajSeqoutCheckGcg(const AjPSeqout outseq);
__deprecated void ajSeqoutDefName(AjPSeqout thys,
const AjPStr setname, AjBool multi);
__deprecated void ajSeqWriteXyz(AjPFile outf,
const AjPStr seq, const char *prefix);
__deprecated void ajSssWriteXyz(AjPFile outf,
const AjPStr seq, const char *prefix);
#endif /* AJ_COMPILE_DEPRECATED */
AJ_END_DECLS
#endif /* !AJSEQWRITE_H */
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