/usr/lib/emboss/include/ajreport.h is in emboss-lib 6.6.0-1.
This file is owned by root:root, with mode 0o644.
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**
** AJAX REPORT (ajax feature reporting) functions
**
** These functions report AJAX sequence feature data in a variety
** of formats.
**
** @author Copyright (C) 2000 Peter Rice, LION Bioscience Ltd.
** @version $Revision: 1.40 $
** @modified Nov 10 First version
** @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 AJREPORT_H
#define AJREPORT_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajmath.h"
#include "ajstr.h"
#include "ajfile.h"
#include "ajlist.h"
#include "ajfeatdata.h"
#include "ajseqdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @data AjPReport ************************************************************
**
** Ajax Report Output object.
**
** Holds definition of feature report output.
**
** @alias AjSReport
** @alias AjOReport
**
** @other AjPSeqout Sequence output
** @other AjPFile Input and output files
**
** @attr Name [AjPStr] As "Source" for features, usually empty
** @attr Type [AjPStr] "P" Protein or "N" Nucleotide
** @attr Formatstr [AjPStr] Report format (-rformat)
** @attr Fttable [AjPFeattable] Feature table to use (obsolete?)
** @attr Ftquery [AjPFeattabOut] Output definition for features
** @attr Extension [AjPStr] Output file extension
** @attr File [AjPFile] Output file object
** @attr Tagnames [AjPList] List of extra tag names (from ACD)
** @attr Tagprints [AjPList] List of extra tag printnames (from ACD)
** @attr Tagtypes [AjPList] List of extra tag datatypes (from ACD)
** @attr Header [AjPStr] Text to add to header with newlines
** @attr SubHeader [AjPStr] Text to add to subheader with newlines
** @attr Tail [AjPStr] Text to add to tail with newlines
** @attr SubTail [AjPStr] Text to add to subtail with newlines
** @attr FileNames [AjPList] Names of extra files (see FileTypes)
** @attr FileTypes [AjPList] Types of extra files (see FileNames)
** @attr Totseqs [ajlong] Total number of sequences processed
** @attr Totlength [ajlong] Total length of sequences processed
** @attr Precision [ajint] Floating precision for score
** @attr Showacc [AjBool] Report accession number
** @attr Showdes [AjBool] Report sequence description
** @attr Showusa [AjBool] Report USA (-rusa) or only seqname
** @attr Showscore [AjBool] Report score (if optional for format)
** @attr Showstrand [AjBool] Report nucleotide strand (if optional for format)
** @attr Multi [AjBool] if true, assume >1 sequence
** @attr Mintags [ajint] Minimum number of tags to report
** @attr CountSeq [ajint] Number of sequences reported so far
** @attr CountHit [ajint] Number of features reported so far
** @attr TotHits [ajint] Number of features found so far
** @attr MaxHitAll [ajint] Maximum number of hits to report overall
** @attr MaxHitSeq [ajint] Maximum number of hits to report for each sequence
** @attr MaxLimit [AjBool] if true, maximum hits reached
** @attr Format [AjEnum] Report format (index number)
** @attr Padding [char[4]] Padding to alignment boundary
**
** @new ajReportNew Default constructor
** @delete ajReportDel Default destructor
** @output ajReportWrite Master sequence output routine
** @@
******************************************************************************/
typedef struct AjSReport {
AjPStr Name;
AjPStr Type;
AjPStr Formatstr;
AjPFeattable Fttable;
AjPFeattabOut Ftquery;
AjPStr Extension;
AjPFile File;
AjPList Tagnames;
AjPList Tagprints;
AjPList Tagtypes;
AjPStr Header;
AjPStr SubHeader;
AjPStr Tail;
AjPStr SubTail;
AjPList FileNames;
AjPList FileTypes;
ajlong Totseqs;
ajlong Totlength;
ajint Precision;
AjBool Showacc;
AjBool Showdes;
AjBool Showusa;
AjBool Showscore;
AjBool Showstrand;
AjBool Multi;
ajint Mintags;
ajint CountSeq;
ajint CountHit;
ajint TotHits;
ajint MaxHitAll;
ajint MaxHitSeq;
AjBool MaxLimit;
AjEnum Format;
char Padding[4];
} AjOReport;
#define AjPReport AjOReport*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
void ajReportClose(AjPReport pthys);
void ajReportDel(AjPReport* pthys);
void ajReportDummyFunction(void);
void ajReportExit(void);
void ajReportAddFileF(AjPReport thys,
AjPFile file, const AjPStr type);
AjBool ajReportFindFormat(const AjPStr format, ajint* iformat);
AjBool ajReportFormatDefault(AjPStr* pformat);
AjPReport ajReportNew(void);
AjBool ajReportOpen(AjPReport thys, const AjPStr name);
void ajReportPrintFormat(AjPFile outf, AjBool full);
void ajReportPrintbookFormat(AjPFile outf);
void ajReportPrinthtmlFormat(AjPFile outf);
void ajReportPrintwikiFormat(AjPFile outf);
const AjPStr ajReportGetSeqnameSeq(const AjPReport thys, const AjPSeq seq);
void ajReportAppendHeaderS(AjPReport thys, const AjPStr header);
void ajReportAppendHeaderC(AjPReport thys, const char* header);
void ajReportSetHeaderS(AjPReport thys, const AjPStr header);
void ajReportSetHeaderC(AjPReport thys, const char* header);
void ajReportAppendSubheaderS(AjPReport thys, const AjPStr header);
void ajReportAppendSubheaderC(AjPReport thys, const char* header);
void ajReportSetSubheaderC(AjPReport thys, const char* header);
void ajReportSetSubheaderS(AjPReport thys, const AjPStr header);
void ajReportSetSeqstats(AjPReport thys, const AjPSeqall seqall);
void ajReportSetSeqsetstats(AjPReport thys, const AjPSeqset seqset);
void ajReportSetStatistics(AjPReport thys, ajlong totseqs,
ajlong totlength);
AjBool ajReportSetTagsS(AjPReport thys, const AjPStr taglist);
void ajReportAppendTailS(AjPReport thys, const AjPStr tail);
void ajReportAppendTailC(AjPReport thys, const char* tail);
void ajReportSetTailS(AjPReport thys, const AjPStr tail);
void ajReportSetTailC(AjPReport thys, const char* tail);
void ajReportAppendSubtailS(AjPReport thys, const AjPStr tail);
void ajReportAppendSubtailC(AjPReport thys, const char* tail);
void ajReportSetSubtailS(AjPReport thys, const AjPStr tail);
void ajReportSetSubtailC(AjPReport thys, const char* tail);
void ajReportSetType(AjPReport thys,
const AjPFeattable ftable, const AjPSeq seq);
AjBool ajReportValid(AjPReport thys);
AjBool ajReportWrite(AjPReport thys,
const AjPFeattable ftable, const AjPSeq seq);
void ajReportWriteHeader(AjPReport thys,
const AjPFeattable ftable, const AjPSeq seq);
void ajReportWriteTail(AjPReport thys,
const AjPFeattable ftable, const AjPSeq seq);
/*
** End of prototype definitions
*/
#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */
#ifdef AJ_COMPILE_DEPRECATED
__deprecated void ajReportFileAdd(AjPReport thys,
AjPFile file, const AjPStr type);
__deprecated void ajReportAppendSubHeader(AjPReport thys,
const AjPStr header);
__deprecated void ajReportAppendSubHeaderC(AjPReport thys,
const char* header);
__deprecated void ajReportSetSubHeader(AjPReport thys,
const AjPStr header);
__deprecated AjBool ajReportSetTags(AjPReport thys,
const AjPStr taglist);
__deprecated void ajReportAppendTail(AjPReport thys, const AjPStr tail);
__deprecated void ajReportSetTail(AjPReport thys, const AjPStr tail);
__deprecated void ajReportAppendHeader(AjPReport thys,
const AjPStr header);
__deprecated void ajReportSetHeader(AjPReport thys, const AjPStr header);
__deprecated void ajReportAppendSubTail(AjPReport thys, const AjPStr tail);
__deprecated void ajReportAppendSubTailC(AjPReport thys, const char* tail);
__deprecated void ajReportSetSubTail(AjPReport thys, const AjPStr tail);
__deprecated void ajReportSetSubTailC(AjPReport thys, const char* tail);
__deprecated const AjPStr ajReportSeqName(const AjPReport thys,
const AjPSeq seq);
__deprecated ajint ajReportLists(const AjPReport thys,
AjPStr** types, AjPStr** names,
AjPStr** prints, ajuint** tagsizes);
#endif /* AJ_COMPILE_DEPRECATED */
AJ_END_DECLS
#endif /* !AJREPORT_H */
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