/usr/lib/emboss/include/ajassem.h is in emboss-lib 6.6.0+dfsg-1.
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 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 | /* @include ajassem ***********************************************************
**
** AJAX assembly functions
**
** These functions control all aspects of AJAX assembly
** parsing and include simple utilities.
**
** @author Copyright (C) 2010 Peter Rice
** @version $Revision: 1.12 $
** @modified Oct 5 pmr First version
** @modified $Date: 2012/03/12 17:42:29 $ 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 AJASSEM_H
#define AJASSEM_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajstr.h"
#include "ajassemdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
AjPAssem ajAssemNew(void);
void ajAssemDel(AjPAssem *Passem);
void ajAssemClear(AjPAssem assem);
void ajAssemReset(AjPAssem assem);
const AjPStr ajAssemGetId(const AjPAssem assem);
const char* ajAssemGetQryC(const AjPAssem assem);
const AjPStr ajAssemGetQryS(const AjPAssem assem);
void ajAssemExit(void);
const char* ajAssemreadgroupGetPlatformname(const AjPAssemReadgroup rg);
AjEAssemPlatform ajAssemplatformGetType(const char* platfname);
const char* ajAssemGetSortorderC(const AjPAssem assem);
AjEAssemSortOrder ajAssemsortorderGetType(const char* name);
void ajAssemSetContigattributes(AjPAssem assem,
const AjPTable tags);
void ajAssemSetReadgroups(AjPAssem assem,
const AjPTable tags);
void ajAssemreadDel(AjPAssemRead *Passemread);
ajint ajAssemreadGetAlignmentend(const AjPAssemRead r);
ajint ajAssemreadGetAlignmentstart(const AjPAssemRead r);
AjBool ajAssemreadGetFlagFirstofpair(const AjPAssemRead r);
AjBool ajAssemreadGetFlagNegativestrand(const AjPAssemRead r);
AjBool ajAssemreadGetFlagPaired(const AjPAssemRead r);
AjBool ajAssemreadGetFlagUnmapped(const AjPAssemRead r);
AjPList ajAssemreadSetAlignblocks(AjPAssemRead read);
/*
** End of prototype definitions
*/
AJ_END_DECLS
#endif /* !AJASSEM_H */
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