ajreport.c

Synopsis

Prototype

void ajReportDel (
      AjPReport* pthys
);

Type Name Read/Write Description

AjPReport* pthys Delete Report object reference

void RETURN

Type	Name	Read/Write	Description
AjPReport*	pthys	Delete	Report object reference
void		RETURN

Output

pthys:

(Delete)

Report object reference

Returns

void:

No return value

Description

Destructor for report objects

Availability

In release 6.4.0

Synopsis

Prototype

AjBool ajReportOpen (
      AjPReport thys,
      const AjPStr name
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr name Input File name

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const AjPStr	name	Input	File name
AjBool		RETURN	ajTrue on success

Input

name:

(Input)

File name

Input & Output

thys:

(Modify)

Report object

Returns

AjBool:

ajTrue on success

Description

Opens a new report file

Availability

In release 6.4.0

Function ajReportFormatDefault

Sets the default format for a feature report

Synopsis

Prototype

AjBool ajReportFormatDefault (
      AjPStr* pformat
);

Type Name Read/Write Description

AjPStr* pformat Output Default format returned

AjBool RETURN ajTrue is format was returned

Type	Name	Read/Write	Description
AjPStr*	pformat	Output	Default format returned
AjBool		RETURN	ajTrue is format was returned

Output

pformat:

(Output)

Default format returned

Returns

AjBool:

ajTrue is format was returned

Description

Sets the default format for a feature report

Availability

In release 6.4.0

Function ajReportFindFormat

Looks for the specified report format in the internal definitions and returns the index.

Synopsis

Prototype

AjBool ajReportFindFormat (
      const AjPStr format,
      ajint* iformat
);

Type Name Read/Write Description

const AjPStr format Input Format required.

ajint* iformat Output Index

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
const AjPStr	format	Input	Format required.
ajint*	iformat	Output	Index
AjBool		RETURN	ajTrue on success.

Input

format:

(Input)

Format required.

Output

iformat:

(Output)

Index

Returns

AjBool:

ajTrue on success.

Description

Looks for the specified report format in the internal definitions and returns the index.

Availability

In release 6.4.0

Synopsis

Prototype

AjBool ajReportSetTagsS (
      AjPReport thys,
      const AjPStr taglist
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr taglist Input Tag names list

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const AjPStr	taglist	Input	Tag names list
AjBool		RETURN	ajTrue on success

Input

taglist:

(Input)

Tag names list

Input & Output

thys:

(Modify)

Report object

Returns

AjBool:

ajTrue on success

Description

Sets the tag list for a report

Availability

In release 6.4.0

Function ajReportValid

Test for a report object.

Checks the format works with the number of tags. Checks the format works with the type (protein or nucleotide). Sets the format if not already defined.

Synopsis

Prototype

AjBool ajReportValid (
      AjPReport thys
);

Type Name Read/Write Description

AjPReport thys Modify Report object

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
AjBool		RETURN	ajTrue on success

Input & Output

thys:

(Modify)

Report object

Returns

AjBool:

ajTrue on success

Description

Test for a report object.

Checks the format works with the number of tags. Checks the format works with the type (protein or nucleotide). Sets the format if not already defined.

Availability

In release 6.4.0

Synopsis

Prototype

AjPReport ajReportNew (
      void
);

Type Name Read/Write Description

AjPReport RETURN New report object

Type	Name	Read/Write	Description
AjPReport		RETURN	New report object

Returns

AjPReport:

New report object

Description

Constructor for a report object

Availability

In release 6.4.0

Synopsis

Prototype

AjBool ajReportWrite (
      AjPReport thys,
      const AjPFeattable ftable,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPFeattable ftable Input Feature table object

const AjPSeq seq Input Sequence object

AjBool RETURN True if data was written False if maximum output has already been reached.

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const AjPFeattable	ftable	Input	Feature table object
const AjPSeq	seq	Input	Sequence object
AjBool		RETURN	True if data was written False if maximum output has already been reached.

Input

ftable:	(Input)	Feature table object
seq:	(Input)	Sequence object

Input & Output

thys:

(Modify)

Report object

Returns

AjBool:

True if data was written False if maximum output has already been reached.

Description

Writes a feature report

Availability

In release 6.4.0

Function ajReportClose

Closes a feature report

Synopsis

Prototype

void ajReportClose (
      AjPReport thys
);

Type Name Read/Write Description

AjPReport thys Modify Report object

void RETURN

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
void		RETURN

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Closes a feature report

Availability

In release 6.4.0

Function ajReportWriteHeader

Writes a feature report header and updates internal counters.

Synopsis

Prototype

void ajReportWriteHeader (
      AjPReport thys,
      const AjPFeattable ftable,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPFeattable ftable Input Feature table object

const AjPSeq seq Input Sequence object

void RETURN

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const AjPFeattable	ftable	Input	Feature table object
const AjPSeq	seq	Input	Sequence object
void		RETURN

Input

ftable:	(Input)	Feature table object
seq:	(Input)	Sequence object

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Writes a feature report header and updates internal counters.

Availability

In release 6.4.0

Function ajReportWriteTail

Writes (and clears) a feature report tail

Synopsis

Prototype

void ajReportWriteTail (
      AjPReport thys,
      const AjPFeattable ftable,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPFeattable ftable Input Feature table object

const AjPSeq seq Input Sequence object

void RETURN

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const AjPFeattable	ftable	Input	Feature table object
const AjPSeq	seq	Input	Sequence object
void		RETURN

Input

ftable:	(Input)	Feature table object
seq:	(Input)	Sequence object

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Writes (and clears) a feature report tail

Availability

In release 6.4.0

Function ajReportSetHeaderS

Defines a feature report header

Synopsis

Prototype

void ajReportSetHeaderS (
      AjPReport thys,
      const AjPStr header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr header Input Report header with embedded newlines

void RETURN

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const AjPStr	header	Input	Report header with embedded newlines
void		RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report header

Availability

In release 6.4.0

Function ajReportSetHeaderC

Defines a feature report header

Synopsis

Prototype

void ajReportSetHeaderC (
      AjPReport thys,
      const char* header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* header Input Report header with embedded newlines

void RETURN

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const char*	header	Input	Report header with embedded newlines
void		RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report header

Availability

In release 6.4.0

Function ajReportAppendHeaderC

Appends to a feature report header

Synopsis

Prototype

void ajReportAppendHeaderC (
      AjPReport thys,
      const char* header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* header Input Report header with embedded newlines

void RETURN

Type	Name	Read/Write	Description
AjPReport	thys	Modify	Report object
const char*	header	Input	Report header with embedded newlines
void		RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report header

Availability

In release 6.4.0

Function ajReportAppendHeaderS

Defines a feature report header

Synopsis

Prototype

void ajReportAppendHeaderS (
      AjPReport thys,
      const AjPStr header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr header Input Report header with embedded newlines

void RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report header

Availability

In release 6.4.0

Function ajReportSetSubheaderC

Appends to a feature report subheader

Synopsis

Prototype

void ajReportSetSubheaderC (
      AjPReport thys,
      const char* header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* header Input Report header with embedded newlines

void RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report subheader

Availability

In release 6.4.0

Function ajReportSetSubheaderS

Defines a feature report subheader

Synopsis

Prototype

void ajReportSetSubheaderS (
      AjPReport thys,
      const AjPStr header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr header Input Report header with embedded newlines

void RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report subheader

Availability

In release 6.4.0

Function ajReportAppendSubheaderC

Appends to a feature report subheader

Synopsis

Prototype

void ajReportAppendSubheaderC (
      AjPReport thys,
      const char* header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* header Input Report header with embedded newlines

void RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report subheader

Availability

In release 6.4.0

Function ajReportAppendSubheaderS

Defines a feature report subheader

Synopsis

Prototype

void ajReportAppendSubheaderS (
      AjPReport thys,
      const AjPStr header
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr header Input Report header with embedded newlines

void RETURN

Input

header:

(Input)

Report header with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report subheader

Availability

In release 6.4.0

Function ajReportSetSeqstats

Defines a feature report tail

Synopsis

Prototype

void ajReportSetSeqstats (
      AjPReport thys,
      const AjPSeqall seqall
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPSeqall seqall Input Sequence stream object

void RETURN

Input

seqall:

(Input)

Sequence stream object

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report tail

Availability

In release 6.4.0

Function ajReportSetSeqsetstats

Defines a feature report tail

Synopsis

Prototype

void ajReportSetSeqsetstats (
      AjPReport thys,
      const AjPSeqset seqset
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPSeqset seqset Input Sequence set object

void RETURN

Input

seqset:

(Input)

Sequence set object

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report tail

Availability

In release 6.4.0

Function ajReportSetStatistics

Defines a feature report tail

Synopsis

Prototype

void ajReportSetStatistics (
      AjPReport thys,
      ajlong totseqs,
      ajlong totlength
);

Type Name Read/Write Description

AjPReport thys Modify Report object

ajlong totseqs Input Total number of sequences processed

ajlong totlength Input Total sequence length processed

void RETURN

Input

totseqs:	(Input)	Total number of sequences processed
totlength:	(Input)	Total sequence length processed

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report tail

Availability

In release 6.4.0

Function ajReportSetTailC

Defines a feature report tail

Synopsis

Prototype

void ajReportSetTailC (
      AjPReport thys,
      const char* tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report tail

Availability

In release 6.4.0

Function ajReportSetTailS

Defines a feature report tail

Synopsis

Prototype

void ajReportSetTailS (
      AjPReport thys,
      const AjPStr tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report tail

Availability

In release 6.4.0

Function ajReportAppendTailC

Appends to a feature report tail

Synopsis

Prototype

void ajReportAppendTailC (
      AjPReport thys,
      const char* tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report tail

Availability

In release 6.4.0

Function ajReportAppendTailS

Appends to a feature report tail

Synopsis

Prototype

void ajReportAppendTailS (
      AjPReport thys,
      const AjPStr tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report tail

Availability

In release 6.4.0

Function ajReportSetSubtailC

Defines a feature report subtail

Synopsis

Prototype

void ajReportSetSubtailC (
      AjPReport thys,
      const char* tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report subtail

Availability

In release 6.4.0

Function ajReportSetSubtailS

Defines a feature report subtail

Synopsis

Prototype

void ajReportSetSubtailS (
      AjPReport thys,
      const AjPStr tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Defines a feature report subtail

Availability

In release 6.4.0

Function ajReportAppendSubtailC

Appends to a feature report subtail

Synopsis

Prototype

void ajReportAppendSubtailC (
      AjPReport thys,
      const char* tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const char* tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report subtail

Availability

In release 6.4.0

Function ajReportAppendSubtailS

Appends to a feature report subtail

Synopsis

Prototype

void ajReportAppendSubtailS (
      AjPReport thys,
      const AjPStr tail
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPStr tail Input Report tail with embedded newlines

void RETURN

Input

tail:

(Input)

Report tail with embedded newlines

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Appends to a feature report subtail

Availability

In release 6.4.0

Function ajReportSetType

Sets the report type (if it is not set already)

Synopsis

Prototype

void ajReportSetType (
      AjPReport thys,
      const AjPFeattable ftable,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPReport thys Modify Report object

const AjPFeattable ftable Input Feature table object

const AjPSeq seq Input Sequence object

void RETURN

Input

ftable:	(Input)	Feature table object
seq:	(Input)	Sequence object

Input & Output

thys:

(Modify)

Report object

Returns

void:

No return value

Description

Sets the report type (if it is not set already)

Availability

In release 6.4.0

Function ajReportGetSeqnameSeq

Returns the sequence name or USA depending on the setting in the report object (derived from the ACD and command line -rusa option)

Synopsis

Prototype

const AjPStr ajReportGetSeqnameSeq (
      const AjPReport thys,
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPReport thys Input Report object

const AjPSeq seq Input Sequence object

const AjPStr RETURN Sequence name for this report

Input

thys:	(Input)	Report object
seq:	(Input)	Sequence object

Returns

const AjPStr:

Sequence name for this report

Description

Returns the sequence name or USA depending on the setting in the report object (derived from the ACD and command line -rusa option)

Availability

In release 6.4.0

Function ajReportAddFileF

Adds an additional file name and description to the report.

These will appear in the header as "Additional files" to let the user know that there are associated output files available.

Synopsis

Prototype

void ajReportAddFileF (
      AjPReport thys,
      AjPFile file,
      const AjPStr type
);

Type Name Read/Write Description

AjPReport thys Modify Report object

AjPFile file Modify File

const AjPStr type Input Type (simple text description)

void RETURN

Input

type:

(Input)

Type (simple text description)

Input & Output

thys:	(Modify)	Report object
file:	(Modify)	File

Returns

void:

No return value

Description

Adds an additional file name and description to the report.

These will appear in the header as "Additional files" to let the user know that there are associated output files available.

Availability

In release 6.4.0

Function ajReportPrintFormat

Reports the internal data structures

Synopsis

Prototype

void ajReportPrintFormat (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full report (usually ajFalse)

void RETURN

Input

full:

(Input)

Full report (usually ajFalse)

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the internal data structures

Availability

In release 6.4.0

Function ajReportPrinthtmlFormat

Reports the internal data structures

Synopsis

Prototype

void ajReportPrinthtmlFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the internal data structures

Availability

In release 6.4.0

Function ajReportPrintbookFormat

Reports the report format internals in DocBook format

Synopsis

Prototype

void ajReportPrintbookFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the report format internals in DocBook format

Availability

In release 6.4.0

Function ajReportPrintwikiFormat

Reports the report format internals as wikitext

Synopsis

Prototype

void ajReportPrintwikiFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the report format internals as wikitext

Availability

In release 6.4.0

Function ajReportDummyFunction

Dummy function to catch all unused functions defined in the ajreport source file.

Synopsis

Prototype

void ajReportDummyFunction (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Dummy function to catch all unused functions defined in the ajreport source file.

Availability

In release 6.4.0

Function ajReportExit

Cleans up report processing internal memory

Synopsis

Prototype

void ajReportExit (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Cleans up report processing internal memory

Availability

In release 6.4.0

Type	Name	Read/Write	Description
const AjPReport	thys	Input	Report object
const AjPSeq	seq	Input	Sequence object
const AjPStr		RETURN	Sequence name for this report

Type	Name	Read/Write	Description
AjPFile	outf	Modify	Output file
AjBool	full	Input	Full report (usually ajFalse)
void		RETURN

ajreport.c

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