ajfeatwrite.c

Function ajFeattabOutOpen

Processes the specified UFO, and opens the resulting output file.

If the AjPFeattabOut has a filename, this is used in preference. If not, the ufo is processed.

Synopsis

Prototype
AjBool ajFeattabOutOpen (
      AjPFeattabOut thys,
      const AjPStr ufo
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyFeatures table output object
const AjPStrufoInputUFO feature output specifier
AjBool RETURNajTrue on success

Input
ufo:(Input)UFO feature output specifier
Input & Output
thys:(Modify)Features table output object
Returns
AjBool:ajTrue on success

Description

Processes the specified UFO, and opens the resulting output file.

If the AjPFeattabOut has a filename, this is used in preference. If not, the ufo is processed.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutFile

Returns the feature table output file object

Synopsis

Prototype
AjPFile ajFeattabOutFile (
      const AjPFeattabOut thys
);

TypeNameRead/WriteDescription
const AjPFeattabOutthysInputFeatures table output object
AjPFile RETURNFile object

Input
thys:(Input)Features table output object
Returns
AjPFile:File object

Description

Returns the feature table output file object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutFilename

Returns the name of a feature table output file

Synopsis

Prototype
AjPStr ajFeattabOutFilename (
      const AjPFeattabOut thys
);

TypeNameRead/WriteDescription
const AjPFeattabOutthysInputFeatures table output object
AjPStr RETURNFilename

Input
thys:(Input)Features table output object
Returns
AjPStr:Filename

Description

Returns the name of a feature table output file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutIsOpen

Checks whether feature output file has already been opened

Synopsis

Prototype
AjBool ajFeattabOutIsOpen (
      const AjPFeattabOut thys
);

TypeNameRead/WriteDescription
const AjPFeattabOutthysInputFeatures table output object
AjBool RETURNajTrue if file is open

Input
thys:(Input)Features table output object
Returns
AjBool:ajTrue if file is open

Description

Checks whether feature output file has already been opened

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutIsLocal

Checks whether feature output file has already been opened

Synopsis

Prototype
AjBool ajFeattabOutIsLocal (
      const AjPFeattabOut thys
);

TypeNameRead/WriteDescription
const AjPFeattabOutthysInputFeatures table output object
AjBool RETURNajTrue if file is open

Input
thys:(Input)Features table output object
Returns
AjBool:ajTrue if file is open

Description

Checks whether feature output file has already been opened

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutSet

Processes the specified UFO, and specifies the resulting output file.

Synopsis

Prototype
AjBool ajFeattabOutSet (
      AjPFeattabOut thys,
      const AjPStr ufo
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyFeatures table output object
const AjPStrufoInputUFO feature output specifier
AjBool RETURNajTrue on success

Input
ufo:(Input)UFO feature output specifier
Input & Output
thys:(Modify)Features table output object
Returns
AjBool:ajTrue on success

Description

Processes the specified UFO, and specifies the resulting output file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutSetBasename

Sets the base output filename for feature table output

Synopsis

Prototype
void ajFeattabOutSetBasename (
      AjPFeattabOut thys,
      const AjPStr basename
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyfeature table output
const AjPStrbasenameInputOutput base filename
void RETURN

Input
basename:(Input)Output base filename
Input & Output
thys:(Modify)feature table output
Returns
void:No return value

Description

Sets the base output filename for feature table output

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutSetSeqname

Processes the specified UFO, and specifies the resulting output file.

Synopsis

Prototype
AjBool ajFeattabOutSetSeqname (
      AjPFeattabOut thys,
      const AjPStr name
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyFeatures table output object
const AjPStrnameInputUFO feature output specifier
AjBool RETURNajTrue on success

Input
name:(Input)UFO feature output specifier
Input & Output
thys:(Modify)Features table output object
Returns
AjBool:ajTrue on success

Description

Processes the specified UFO, and specifies the resulting output file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutNewCSF

Constructor for an empty feature table output object, using an existing open output file (the file sequence data is already written to)

Synopsis

Prototype
AjPFeattabOut ajFeattabOutNewCSF (
      const char* fmt,
      const AjPStr name,
      const char* type,
      AjPFile file
);

TypeNameRead/WriteDescription
const char*fmtInputfeature format
const AjPStrnameInputsequence name
const char*typeInputfeature type
AjPFilefileModifyOutput file
AjPFeattabOut RETURNFeature table output object

Input
fmt:(Input)feature format
name:(Input)sequence name
type:(Input)feature type
Input & Output
file:(Modify)Output file
Returns
AjPFeattabOut:Feature table output object

Description

Constructor for an empty feature table output object, using an existing open output file (the file sequence data is already written to)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutNewSSF

Constructor for an empty feature table output object, using an existing open output file (the file sequence data is already written to)

Synopsis

Prototype
AjPFeattabOut ajFeattabOutNewSSF (
      const AjPStr fmt,
      const AjPStr name,
      const char* type,
      AjPFile file
);

TypeNameRead/WriteDescription
const AjPStrfmtInputfeature format
const AjPStrnameInputsequence name
const char*typeInputfeature type
AjPFilefileModifyOutput file
AjPFeattabOut RETURNFeature table output object

Input
fmt:(Input)feature format
name:(Input)sequence name
type:(Input)feature type
Input & Output
file:(Modify)Output file
Returns
AjPFeattabOut:Feature table output object

Description

Constructor for an empty feature table output object, using an existing open output file (the file sequence data is already written to)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutNew

Constructor for an empty feature table output object

Synopsis

Prototype
AjPFeattabOut ajFeattabOutNew (
      void
);

TypeNameRead/WriteDescription
AjPFeattabOut RETURNFeature table input object

Returns
AjPFeattabOut:Feature table input object

Description

Constructor for an empty feature table output object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutClear

Clears all data for a feature table output object

Synopsis

Prototype
void ajFeattabOutClear (
      AjPFeattabOut* thys
);

TypeNameRead/WriteDescription
AjPFeattabOut*thysDeletefeature format
void RETURNFeature table output object

Output
thys:(Delete)feature format
Returns
void:No return value

Description

Clears all data for a feature table output object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutDel

Destructor for a feature table output object

Synopsis

Prototype
void ajFeattabOutDel (
      AjPFeattabOut* thys
);

TypeNameRead/WriteDescription
AjPFeattabOut*thysDeletefeature format
void RETURNFeature table output object

Output
thys:(Delete)feature format
Returns
void:No return value

Description

Destructor for a feature table output object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteUfo

Parses a UFO, opens an output file, and writes a feature table to it.

Synopsis

Prototype
AjBool ajFeattableWriteUfo (
      AjPFeattabOut thys,
      const AjPFeattable ftable,
      const AjPStr ufo
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyFeature output object
const AjPFeattableftableInputFeature table to be written
const AjPStrufoInputUFO feature spec (ignored if already open)
AjBool RETURNajTrue on success.

Input
ftable:(Input)Feature table to be written
ufo:(Input)UFO feature spec (ignored if already open)
Input & Output
thys:(Modify)Feature output object
Returns
AjBool:ajTrue on success.

Description

Parses a UFO, opens an output file, and writes a feature table to it.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatOutFormatDefault

Sets the default output format. Checks the _OUTFEATFORMAT variable, and uses GFF3 if no other definition is found.

Synopsis

Prototype
AjBool ajFeatOutFormatDefault (
      AjPStr* pformat
);

TypeNameRead/WriteDescription
AjPStr*pformatOutputDefault output feature format.
AjBool RETURNajTrue on success.

Output
pformat:(Output)Default output feature format.
Returns
AjBool:ajTrue on success.

Description

Sets the default output format. Checks the _OUTFEATFORMAT variable, and uses GFF3 if no other definition is found.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWrite

Generic interface function for writing features to a file defined by a feature table output object.

Synopsis

Prototype
AjBool ajFeattableWrite (
      AjPFeattabOut ftout,
      const AjPFeattable features
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifySpecifies the external source (file) of the features to be written
const AjPFeattablefeaturesInputFeature set to be written out
AjBool RETURNReturns ajTrue if successful; ajFalse otherwise

Input
features:(Input)Feature set to be written out
Input & Output
ftout:(Modify)Specifies the external source (file) of the features to be written
Returns
AjBool:Returns ajTrue if successful; ajFalse otherwise

Description

Generic interface function for writing features to a file defined by a feature table output object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteGff2

Write feature table in GFF 2.0 format

Synopsis

Prototype
AjBool ajFeattableWriteGff2 (
      AjPFeattabOut ftout,
      const AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattableFeattabInputfeature table
AjBool RETURNajTrue on success

Input
Feattab:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write feature table in GFF 2.0 format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteGff3

Write feature table in GFF format

Synopsis

Prototype
AjBool ajFeattableWriteGff3 (
      AjPFeattabOut ftout,
      const AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattableFeattabInputfeature table
AjBool RETURNajTrue on success

Input
Feattab:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write feature table in GFF format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteDdbj

Write a feature table in DDBJ format.

Synopsis

Prototype
AjBool ajFeattableWriteDdbj (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in DDBJ format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteEmbl

Write a feature table in EMBL format.

Synopsis

Prototype
AjBool ajFeattableWriteEmbl (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in EMBL format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteGenbank

Write a feature table in GenBank format.

Synopsis

Prototype
AjBool ajFeattableWriteGenbank (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in GenBank format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteRefseq

Write a feature table in Refseq format.

Synopsis

Prototype
AjBool ajFeattableWriteRefseq (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in Refseq format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteRefseqp

Write a feature table in Refseqp format.

Synopsis

Prototype
AjBool ajFeattableWriteRefseqp (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in Refseqp format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteSwiss

Write a feature table in SwissProt format.

Synopsis

Prototype
AjBool ajFeattableWriteSwiss (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in SwissProt format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWritePir

Write a feature table in PIR format.

Synopsis

Prototype
AjBool ajFeattableWritePir (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputfeature table
AjBool RETURNajTrue on success

Input
thys:(Input)feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in PIR format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteDasgff

Write a feature table in DAS GFF format.

Synopsis

Prototype
AjBool ajFeattableWriteDasgff (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattablethysInputFeature table
AjBool RETURNajTrue on success

Input
thys:(Input)Feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:ajTrue on success

Description

Write a feature table in DAS GFF format.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutSetType

Sets the type for feature output

Synopsis

Prototype
AjBool ajFeattabOutSetType (
      AjPFeattabOut thys,
      const AjPStr type
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyFeature output object
const AjPStrtypeInputFeature type "nucleotide" "protein"
AjBool RETURNajTrue on success

Input
type:(Input)Feature type "nucleotide" "protein"
Input & Output
thys:(Modify)Feature output object
Returns
AjBool:ajTrue on success

Description

Sets the type for feature output

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattabOutSetTypeC

Sets the type for feature output

Synopsis

Prototype
AjBool ajFeattabOutSetTypeC (
      AjPFeattabOut thys,
      const char* type
);

TypeNameRead/WriteDescription
AjPFeattabOutthysModifyFeature output object
const char*typeInputFeature type "nucleotide" "protein"
AjBool RETURNajTrue on success

Input
type:(Input)Feature type "nucleotide" "protein"
Input & Output
thys:(Modify)Feature output object
Returns
AjBool:ajTrue on success

Description

Sets the type for feature output

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableWriteDebug

Print contents of a feature table to a file

Synopsis

Prototype
AjBool ajFeattableWriteDebug (
      AjPFeattabOut ftout,
      const AjPFeattable ftable
);

TypeNameRead/WriteDescription
AjPFeattabOutftoutModifyFeature table output object
const AjPFeattableftableInputFeature table
AjBool RETURNAlways true

Input
ftable:(Input)Feature table
Input & Output
ftout:(Modify)Feature table output object
Returns
AjBool:Always true

Description

Print contents of a feature table to a file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattablePrint

Print contents of a feature table to a file

Synopsis

Prototype
AjBool ajFeattablePrint (
      const AjPFeattable ftable,
      AjPFile outf
);

TypeNameRead/WriteDescription
const AjPFeattableftableInputFeature table
AjPFileoutfModifyOutput file object
AjBool RETURNAlways true

Input
ftable:(Input)Feature table
Input & Output
outf:(Modify)Output file object
Returns
AjBool:Always true

Description

Print contents of a feature table to a file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatoutPrintFormat

Reports the internal data structures for output feature formats

Synopsis

Prototype
void ajFeatoutPrintFormat (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull 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 for output feature formats

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatoutPrinthtmlFormat

Reports the internal data structures for output feature formats

Synopsis

Prototype
void ajFeatoutPrinthtmlFormat (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the internal data structures for output feature formats

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatoutPrintbookFormat

Reports the output feature format internals in docbook format

Synopsis

Prototype
void ajFeatoutPrintbookFormat (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the output feature format internals in docbook format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatoutPrintwikiFormat

Reports the output feature format internals in wiki text format

Synopsis

Prototype
void ajFeatoutPrintwikiFormat (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the output feature format internals in wiki text format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatwriteExit

Cleans up feature table output internal memory

Synopsis

Prototype
void ajFeatwriteExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up feature table output internal memory

See Also

See other functions in this section

Availability

In release 6.4.0