emboss-lib 6.3.1-6ubuntu3 / usr / lib / emboss / include / ajreport.h

#ifdef __cplusplus
extern "C"
{
#endif

#ifndef ajseqreport_h
#define ajseqreport_h




/* @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*




/*
** 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         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
*/

__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

#ifdef __cplusplus
}
#endif