ajfeat.c

Section: Feature Object Constructors

Generally, however, the AjPFeattable feature table object will first be created, prior to creating any 'AjPFeature' objects and adding them.

To replace or reuse an existing feature object see instead the Feature Assignments and Feature Modifiers methods.

Functions: ajFeattabOutOpen ajFeattabOutFile ajFeattabOutFilename ajFeattabOutIsOpen ajFeattabOutIsLocal ajFeattabOutSet ajFeattabInNew ajFeattabInNewSS ajFeattabInNewCSF ajFeattabInNewSSF ajFeattabOutNew ajFeattabOutSetBasename ajFeattabOutSetSeqname ajFeattabOutNewCSF ajFeattabOutNewSSF ajFeatRead ajFeatNew ajFeatNewII ajFeatNewIIRev ajFeatNewProt

Function ajFeattabOutOpen

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
);

Type	Name	Read/Write	Description
AjPFeattabOut	thys	Modify	Features table output object
const AjPStr	ufo	Input	UFO feature output specifier
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

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

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutFile

Synopsis

Prototype

AjPFile ajFeattabOutFile (
      const AjPFeattabOut thys
);

Type	Name	Read/Write	Description
const AjPFeattabOut	thys	Input	Features table output object
AjPFile		RETURN	File object

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutFilename

Synopsis

Prototype

AjPStr ajFeattabOutFilename (
      const AjPFeattabOut thys
);

Type	Name	Read/Write	Description
const AjPFeattabOut	thys	Input	Features table output object
AjPStr		RETURN	Filename

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutIsOpen

Synopsis

Prototype

AjBool ajFeattabOutIsOpen (
      const AjPFeattabOut thys
);

Type	Name	Read/Write	Description
const AjPFeattabOut	thys	Input	Features table output object
AjBool		RETURN	ajTrue if file is open

Input

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattabOutIsLocal

Synopsis

Prototype

AjBool ajFeattabOutIsLocal (
      const AjPFeattabOut thys
);

Type	Name	Read/Write	Description
const AjPFeattabOut	thys	Input	Features table output object
AjBool		RETURN	ajTrue if file is open

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutSet

Synopsis

Prototype

AjBool ajFeattabOutSet (
      AjPFeattabOut thys,
      const AjPStr ufo
);

Type	Name	Read/Write	Description
AjPFeattabOut	thys	Modify	Features table output object
const AjPStr	ufo	Input	UFO feature output specifier
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInNew

Synopsis

Prototype

AjPFeattabIn ajFeattabInNew (
      void
);

Type	Name	Read/Write	Description
AjPFeattabIn		RETURN	Feature table input object

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInNewSS

Synopsis

Prototype

AjPFeattabIn ajFeattabInNewSS (
      const AjPStr fmt,
      const AjPStr name,
      const char* type
);

Type	Name	Read/Write	Description
const AjPStr	fmt	Input	feature format
const AjPStr	name	Input	sequence name
const char*	type	Input	feature type
AjPFeattabIn		RETURN	Feature table input object

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInNewCSF

Synopsis

Prototype

AjPFeattabIn ajFeattabInNewCSF (
      const char* fmt,
      const AjPStr name,
      const char* type,
      AjPFilebuff buff
);

Type	Name	Read/Write	Description
const char*	fmt	Input	feature format
const AjPStr	name	Input	sequence name
const char*	type	Input	feature type
AjPFilebuff	buff	Modify	Buffer containing feature data
AjPFeattabIn		RETURN	Feature table input object

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInNewSSF

Synopsis

Prototype

AjPFeattabIn ajFeattabInNewSSF (
      const AjPStr fmt,
      const AjPStr name,
      const char* type,
      AjPFilebuff buff
);

Type	Name	Read/Write	Description
const AjPStr	fmt	Input	feature format
const AjPStr	name	Input	sequence name
const char*	type	Input	feature type
AjPFilebuff	buff	Modify	Buffer containing feature data
AjPFeattabIn		RETURN	Feature table input object

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutNew

Synopsis

Prototype

AjPFeattabOut ajFeattabOutNew (
      void
);

Type	Name	Read/Write	Description
AjPFeattabOut		RETURN	Feature table input object

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutSetBasename

Synopsis

Prototype

void ajFeattabOutSetBasename (
      AjPFeattabOut thys,
      const AjPStr basename
);

Type	Name	Read/Write	Description
AjPFeattabOut	thys	Modify	feature table output
const AjPStr	basename	Input	Output base filename
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutSetSeqname

Synopsis

Prototype

AjBool ajFeattabOutSetSeqname (
      AjPFeattabOut thys,
      const AjPStr name
);

Type	Name	Read/Write	Description
AjPFeattabOut	thys	Modify	Features table output object
const AjPStr	name	Input	UFO feature output specifier
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutNewCSF

Synopsis

Prototype

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

Type	Name	Read/Write	Description
const char*	fmt	Input	feature format
const AjPStr	name	Input	sequence name
const char*	type	Input	feature type
AjPFile	file	Modify	Output file
AjPFeattabOut		RETURN	Feature table output object

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutNewSSF

Synopsis

Prototype

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

Type	Name	Read/Write	Description
const AjPStr	fmt	Input	feature format
const AjPStr	name	Input	sequence name
const char*	type	Input	feature type
AjPFile	file	Modify	Output file
AjPFeattabOut		RETURN	Feature table output object

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatRead

Synopsis

Prototype

AjPFeattable ajFeatRead (
      AjPFeattabIn ftin
);

Type	Name	Read/Write	Description
AjPFeattabIn	ftin	Modify	Specifies the external source (file) of the features to be read in
AjPFeattable		RETURN	Pointer to a new feature table containing the features read in

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatNew

Synopsis

Prototype

AjPFeature ajFeatNew (
      AjPFeattable thys,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score,
      char strand,
      ajint frame
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
const AjPStr	source	Input	Analysis basis for feature
const AjPStr	type	Input	Type of feature (e.g. exon)
ajint	Start	Input	Start position of the feature
ajint	End	Input	End position of the feature
float	score	Input	Analysis score for the feature
char	strand	Input	Strand of the feature
ajint	frame	Input	Frame of the feature
AjPFeature		RETURN	newly allocated feature object

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatNewII

User must specify associated 'ajFeattable' to which the new feature is automatically added!

Synopsis

Prototype

AjPFeature ajFeatNewII (
      AjPFeattable thys,
      ajint Start,
      ajint End
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
ajint	Start	Input	Start position of the feature
ajint	End	Input	End position of the feature
AjPFeature		RETURN	newly allocated feature object

Input

Input & Output

Returns

Description

User must specify associated 'ajFeattable' to which the new feature is automatically added!

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatNewIIRev

User must specify associated 'ajFeattable' to which the new feature is automatically added!

Synopsis

Prototype

AjPFeature ajFeatNewIIRev (
      AjPFeattable thys,
      ajint Start,
      ajint End
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
ajint	Start	Input	Start position of the feature
ajint	End	Input	End position of the feature
AjPFeature		RETURN	newly allocated feature object

Input

Input & Output

Returns

Description

User must specify associated 'ajFeattable' to which the new feature is automatically added!

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatNewProt

Synopsis

Prototype

AjPFeature ajFeatNewProt (
      AjPFeattable thys,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
const AjPStr	source	Input	Analysis basis for feature
const AjPStr	type	Input	Type of feature (e.g. exon)
ajint	Start	Input	Start position of the feature
ajint	End	Input	End position of the feature
float	score	Input	Analysis score for the feature
AjPFeature		RETURN	newly allocated feature object

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Section: Feature Object Destructors

No reference counting (for now).

Functions: ajFeattabInDel ajFeattableDel ajFeatDel

Function ajFeattabInDel

Synopsis

Prototype

void ajFeattabInDel (
      AjPFeattabIn* pthis
);

Type	Name	Read/Write	Description
AjPFeattabIn*	pthis	Delete	Feature table input object
void		RETURN

Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableDel

Synopsis

Prototype

void ajFeattableDel (
      AjPFeattable* pthis
);

Type	Name	Read/Write	Description
AjPFeattable*	pthis	Delete	Pointer to the object to be deleted. The pointer is always deleted.
void		RETURN

Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatDel

Synopsis

Prototype

void ajFeatDel (
      AjPFeature* pthis
);

Type	Name	Read/Write	Description
AjPFeature*	pthis	Delete	Pointer to the object to be deleted. The pointer is always deleted.
void		RETURN

Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Section: Feature Assignments

Functions: ajFeatUfoWrite ajFeattableWrite ajFeatSortByType ajFeatSortByStart ajFeatSortByEnd

Function ajFeatUfoWrite

Synopsis

Prototype

AjBool ajFeatUfoWrite (
      const AjPFeattable thys,
      AjPFeattabOut featout,
      const AjPStr ufo
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table to be written
AjPFeattabOut	featout	Modify	Feature output object
const AjPStr	ufo	Input	UFO feature spec (ignored if already open)
AjBool		RETURN	ajTrue on success.

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableWrite

Synopsis

Prototype

AjBool ajFeattableWrite (
      AjPFeattable thys,
      const AjPStr ufo
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Output	Feature table created
const AjPStr	ufo	Input	UFO feature spec
AjBool		RETURN	ajTrue on success.

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatSortByType

Synopsis

Prototype

void ajFeatSortByType (
      AjPFeattable Feattab
);

Type	Name	Read/Write	Description
AjPFeattable	Feattab	Modify	Feature table to be sorted.
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatSortByStart

Synopsis

Prototype

void ajFeatSortByStart (
      AjPFeattable Feattab
);

Type	Name	Read/Write	Description
AjPFeattable	Feattab	Modify	Feature table to be sorted.
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatSortByEnd

Synopsis

Prototype

void ajFeatSortByEnd (
      AjPFeattable Feattab
);

Type	Name	Read/Write	Description
AjPFeattable	Feattab	Modify	Feature table to be sorted.
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

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Availability

Section: Feature Table Modifiers

Functions: ajFeattableAdd

Function ajFeattableAdd

Synopsis

Prototype

void ajFeattableAdd (
      AjPFeattable thys,
      AjPFeature feature
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	The feature table
AjPFeature	feature	Modify	Feature to be added to the set
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Section: Feature Object Operators

Functions: ajFeattableClear ajFeatOutFormatDefault ajFeatWrite ajFeattableWriteGff2 ajFeattableWriteGff3 ajFeattableWriteDdbj ajFeattableWriteEmbl ajFeattableWriteGenbank ajFeattableWriteSwiss ajFeattableWritePir ajFeattableWriteDasgff ajFeattableGetName ajFeattableGetSize ajFeatTypeGetCategory ajFeattableGetTypeC ajFeattableGetTypeS ajFeattableGetXrefs ajFeattableIsNuc ajFeattableIsProt ajFeattableBegin ajFeattableEnd ajFeattableLen ajFeattableSize ajFeattabInClear ajFeatGetSeq ajFeatGetRemoteseq ajFeatGetXrefs ajFeatLocMark ajFeatGetNote ajFeatGetNoteC ajFeatGetNoteCI ajFeatGetNoteI ajFeatGetTagC ajFeatGetTagS ajFeatGetType ajFeatGetSource ajFeatGetStart ajFeatGetStrand ajFeatGetEnd ajFeatGetLength ajFeatGetScore ajFeatGetForward ajFeatGetFrame ajFeatGetTranslation ajFeatTest ajFeatSetDescApp ajFeatSetDesc ajFeatSetScore ajFeatSetStrand ajFeattabInSetType ajFeattabInSetTypeC ajFeattabOutSetType ajFeattabOutSetTypeC ajFeatTagSetC ajFeatTagSet ajFeatTagAddCC ajFeatTagAddC ajFeatTagAdd ajFeattableNew ajFeatUfoRead ajFeattableSetLength ajFeattableSetNuc ajFeattableSetProt ajFeattableReverse ajFeatReverse ajFeattableSetRange ajFeattableNewDna ajFeattableNewSeq ajFeattableNewProt ajFeattableCopy ajFeattableCopyLimit ajFeatCopy ajFeatTrace ajFeatTagTrace ajFeatTagIter ajFeatTagval ajFeattableTrace ajFeatTypeNuc ajFeatTypeProt ajFeatExit ajFeatUnused ajFeatTypeIsCds ajFeatTypeMatchC ajFeatTypeMatchS ajFeatIsLocal ajFeatIsLocalRange ajFeatIsChild ajFeatIsMultiple ajFeatIsCompMult ajFeattabOutClear ajFeattabOutDel ajFeattablePos ajFeattablePosI ajFeattablePosII ajFeattableTrimOff ajFeatTrimOffRange ajFeatDefName ajFeattableWriteDebug ajFeattablePrint ajFeatPrintFormat ajFeattagIsNote

Function ajFeattableClear

Synopsis

Prototype

void ajFeattableClear (
      AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatOutFormatDefault

Synopsis

Prototype

AjBool ajFeatOutFormatDefault (
      AjPStr* pformat
);

Type	Name	Read/Write	Description
AjPStr*	pformat	Output	Default output feature format.
AjBool		RETURN	ajTrue on success.

Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeatWrite

Synopsis

Prototype

AjBool ajFeatWrite (
      AjPFeattabOut ftout,
      const AjPFeattable features
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Specifies the external source (file) of the features to be written
const AjPFeattable	features	Input	Feature set to be written out
AjBool		RETURN	Returns ajTrue if successful; ajFalse otherwise

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableWriteGff2

Synopsis

Prototype

AjBool ajFeattableWriteGff2 (
      AjPFeattabOut ftout,
      const AjPFeattable Feattab
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	Feattab	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableWriteGff3

Synopsis

Prototype

AjBool ajFeattableWriteGff3 (
      AjPFeattabOut ftout,
      const AjPFeattable Feattab
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	Feattab	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableWriteDdbj

Synopsis

Prototype

AjBool ajFeattableWriteDdbj (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	thys	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableWriteEmbl

Synopsis

Prototype

AjBool ajFeattableWriteEmbl (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	thys	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableWriteGenbank

Synopsis

Prototype

AjBool ajFeattableWriteGenbank (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	thys	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableWriteSwiss

Synopsis

Prototype

AjBool ajFeattableWriteSwiss (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	thys	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableWritePir

Synopsis

Prototype

AjBool ajFeattableWritePir (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	thys	Input	feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableWriteDasgff

Synopsis

Prototype

AjBool ajFeattableWriteDasgff (
      AjPFeattabOut ftout,
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	thys	Input	Feature table
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableGetName

Synopsis

Prototype

const AjPStr ajFeattableGetName (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
const AjPStr		RETURN	Feature table name.

Input

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableGetSize

Synopsis

Prototype

ajuint ajFeattableGetSize (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
ajuint		RETURN	Feature table size.

Input

Returns

Description

Usage

Example

Errors

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Availability

Function ajFeatTypeGetCategory

Used to identify category for DASGFF output

Synopsis

Prototype

const AjPStr ajFeatTypeGetCategory (
      const AjPStr type
);

Type	Name	Read/Write	Description
const AjPStr	type	Input	Feature type
const AjPStr		RETURN	Feature category

Input

Returns

Description

Used to identify category for DASGFF output

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableGetTypeC

Synopsis

Prototype

const char* ajFeattableGetTypeC (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
const char*		RETURN	Feature table type.

Input

Returns

Description

Usage

Example

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Function ajFeattableGetTypeS

Synopsis

Prototype

const AjPStr ajFeattableGetTypeS (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
const AjPStr		RETURN	Feature table name.

Input

Returns

Description

Usage

Example

Errors

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Availability

Function ajFeattableGetXrefs

Synopsis

Prototype

AjBool ajFeattableGetXrefs (
      const AjPFeattable thys,
      AjPList xreflist,
      ajuint* Ptaxid
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
AjPList	xreflist	Modify	List of sequence cross-reference objects
ajuint*	Ptaxid	Output	Taxon ID
AjBool		RETURN	True on success

Input

Output

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

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Availability

Function ajFeattableIsNuc

Synopsis

Prototype

AjBool ajFeattableIsNuc (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
AjBool		RETURN	ajTrue for a protein feature table

Input

Returns

Description

Usage

Example

Errors

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Availability

Function ajFeattableIsProt

Synopsis

Prototype

AjBool ajFeattableIsProt (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
AjBool		RETURN	ajTrue for a protein feature table

Input

Returns

Description

Usage

Example

Errors

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Availability

Function ajFeattableBegin

Synopsis

Prototype

ajint ajFeattableBegin (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	feature table object
ajint		RETURN	Start position.

Input

Returns

Description

Usage

Example

Errors

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Availability

Function ajFeattableEnd

Synopsis

Prototype

ajint ajFeattableEnd (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	feature table object
ajint		RETURN	End position.

Input

Returns

Description

Usage

Example

Errors

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Availability

Function ajFeattableLen

Synopsis

Prototype

ajint ajFeattableLen (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
ajint		RETURN	Length in bases or residues

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableSize

Synopsis

Prototype

ajint ajFeattableSize (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
ajint		RETURN	Number of features

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInClear

Synopsis

Prototype

void ajFeattabInClear (
      AjPFeattabIn thys
);

Type	Name	Read/Write	Description
AjPFeattabIn	thys	Modify	Sequence input
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetSeq

The database name is used to retrieve sequences from other entries

Synopsis

Prototype

AjBool ajFeatGetSeq (
      const AjPFeature thys,
      const AjPFeattable table,
      const AjPSeq seq,
      AjPStr* Pseqstr
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
const AjPFeattable	table	Input	Full feature table
const AjPSeq	seq	Input	Sequence for the current feature table
AjPStr*	Pseqstr	Modify	Sequence for this feature
AjBool		RETURN	True on success

Input

Input & Output

Returns

Description

The database name is used to retrieve sequences from other entries

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetRemoteseq

Synopsis

Prototype

AjBool ajFeatGetRemoteseq (
      const AjPFeature thys,
      const AjPStr usa,
      AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
const AjPStr	usa	Input	usa of query
AjPSeq	seq	Modify	Sequence object for results
AjBool		RETURN	True on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetXrefs

Synopsis

Prototype

AjBool ajFeatGetXrefs (
      const AjPFeature thys,
      AjPList xreflist
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
AjPList	xreflist	Modify	List of sequence cross-reference objects
AjBool		RETURN	True on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatLocMark

Synopsis

Prototype

AjBool ajFeatLocMark (
      const AjPFeature thys,
      const AjPFeattable table,
      AjPStr* Pseqstr
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
const AjPFeattable	table	Input	Feature table
AjPStr*	Pseqstr	Modify	Sequence to be marked in lower case
AjBool		RETURN	true on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetNote

Synopsis

Prototype

AjBool ajFeatGetNote (
      const AjPFeature thys,
      const AjPStr name,
      AjPStr* val
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const AjPStr	name	Input	Tag name
AjPStr*	val	Output	Tag value (if found)
AjBool		RETURN	ajTrue on success (feature tag found)

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetNoteC

Synopsis

Prototype

AjBool ajFeatGetNoteC (
      const AjPFeature thys,
      const char* name,
      AjPStr* val
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const char*	name	Input	Tag name
AjPStr*	val	Output	Tag value (if found)
AjBool		RETURN	ajTrue on success (feature tag found)

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetNoteCI

Synopsis

Prototype

AjBool ajFeatGetNoteCI (
      const AjPFeature thys,
      const char* name,
      ajint count,
      AjPStr* val
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const char*	name	Input	Tag name
ajint	count	Input	Tag count: zero for any, 1 for first, 2 for second
AjPStr*	val	Output	Tag value (if found)
AjBool		RETURN	ajTrue on success (feature tag found)

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetNoteI

Synopsis

Prototype

AjBool ajFeatGetNoteI (
      const AjPFeature thys,
      const AjPStr name,
      ajint count,
      AjPStr* val
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const AjPStr	name	Input	Tag name
ajint	count	Input	Tag count: zero for any, 1 for first, 2 for second
AjPStr*	val	Output	Tag value (if found)
AjBool		RETURN	ajTrue on success (feature tag found)

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetTagC

If not found as a tag, also searches for a named note

Synopsis

Prototype

AjBool ajFeatGetTagC (
      const AjPFeature thys,
      const char* tname,
      ajint num,
      AjPStr* Pval
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const char*	tname	Input	Tag name
ajint	num	Input	Tag number
AjPStr*	Pval	Output	Tag value (if found)
AjBool		RETURN	ajTrue on success (feature tag found)

Input

Output

Returns

Description

If not found as a tag, also searches for a named note

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetTagS

If not found as a tag, also searches for a named note

Synopsis

Prototype

AjBool ajFeatGetTagS (
      const AjPFeature thys,
      const AjPStr name,
      ajint num,
      AjPStr* val
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const AjPStr	name	Input	Tag name
ajint	num	Input	Tag number
AjPStr*	val	Output	Tag value (if found)
AjBool		RETURN	ajTrue on success (feature tag found)

Input

Output

Returns

Description

If not found as a tag, also searches for a named note

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetType

Synopsis

Prototype

const AjPStr ajFeatGetType (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const AjPStr		RETURN	Feature type, read only

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetSource

Synopsis

Prototype

const AjPStr ajFeatGetSource (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
const AjPStr		RETURN	Feature source name

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetStart

Synopsis

Prototype

ajuint ajFeatGetStart (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
ajuint		RETURN	Feature start position

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetStrand

Synopsis

Prototype

char ajFeatGetStrand (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
char		RETURN	Feature strand code

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetEnd

Synopsis

Prototype

ajuint ajFeatGetEnd (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
ajuint		RETURN	Feature end position

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetLength

Synopsis

Prototype

ajuint ajFeatGetLength (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
ajuint		RETURN	Feature length

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetScore

Synopsis

Prototype

float ajFeatGetScore (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
float		RETURN	Feature score

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetForward

Synopsis

Prototype

AjBool ajFeatGetForward (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
AjBool		RETURN	ajTrue for a forward direction, ajFalse for reverse

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetFrame

Synopsis

Prototype

ajint ajFeatGetFrame (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature object
ajint		RETURN	Feature reading frame (zero for undefined)

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatGetTranslation

Synopsis

Prototype

AjBool ajFeatGetTranslation (
      const AjPFeature thys,
      AjPStr* Ptrans
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
AjPStr*	Ptrans	Output	Translations
AjBool		RETURN	True if translation tag was found

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTest

Synopsis

Prototype

void ajFeatTest (
      void
);

Type	Name	Read/Write	Description
void		RETURN

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatSetDescApp

Synopsis

Prototype

void ajFeatSetDescApp (
      AjPFeature thys,
      const AjPStr desc
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const AjPStr	desc	Input	Feature description (simple text)
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatSetDesc

Synopsis

Prototype

void ajFeatSetDesc (
      AjPFeature thys,
      const AjPStr desc
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const AjPStr	desc	Input	Feature description (simple text)
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatSetScore

Synopsis

Prototype

void ajFeatSetScore (
      AjPFeature thys,
      float score
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
float	score	Input	Score value
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatSetStrand

Synopsis

Prototype

void ajFeatSetStrand (
      AjPFeature thys,
      AjBool rev
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
AjBool	rev	Input	True if reverse strand
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInSetType

Synopsis

Prototype

AjBool ajFeattabInSetType (
      AjPFeattabIn thys,
      const AjPStr type
);

Type	Name	Read/Write	Description
AjPFeattabIn	thys	Modify	Feature input object
const AjPStr	type	Input	Feature type "nucleotide" "protein"
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabInSetTypeC

Synopsis

Prototype

AjBool ajFeattabInSetTypeC (
      AjPFeattabIn thys,
      const char* type
);

Type	Name	Read/Write	Description
AjPFeattabIn	thys	Modify	Feature input object
const char*	type	Input	Feature type "nucleotide" "protein"
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutSetType

Synopsis

Prototype

AjBool ajFeattabOutSetType (
      AjPFeattabOut thys,
      const AjPStr type
);

Type	Name	Read/Write	Description
AjPFeattabOut	thys	Modify	Feature output object
const AjPStr	type	Input	Feature type "nucleotide" "protein"
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattabOutSetTypeC

Synopsis

Prototype

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

Type	Name	Read/Write	Description
AjPFeattabOut	thys	Modify	Feature output object
const char*	type	Input	Feature type "nucleotide" "protein"
AjBool		RETURN	ajTrue on success

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagSetC

Synopsis

Prototype

AjBool ajFeatTagSetC (
      AjPFeature thys,
      const char* tag,
      const AjPStr value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const char*	tag	Input	Feature tag
const AjPStr	value	Input	Feature tag value
AjBool		RETURN	ajTrue is value was valid ajFalse if it was "corrceted"

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagSet

Synopsis

Prototype

AjBool ajFeatTagSet (
      AjPFeature thys,
      const AjPStr tag,
      const AjPStr value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const AjPStr	tag	Input	Feature tag
const AjPStr	value	Input	Feature tag value
AjBool		RETURN	ajTrue is value was valid ajFalse if it was "corrceted"

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagAddCC

Synopsis

Prototype

AjBool ajFeatTagAddCC (
      AjPFeature thys,
      const char* tag,
      const char* value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const char*	tag	Input	Feature tag
const char*	value	Input	Feature tag value
AjBool		RETURN	ajTrue if value was valid ajFalse if it was bad and was "corrected"

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagAddC

Synopsis

Prototype

AjBool ajFeatTagAddC (
      AjPFeature thys,
      const char* tag,
      const AjPStr value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const char*	tag	Input	Feature tag
const AjPStr	value	Input	Feature tag value
AjBool		RETURN	ajTrue if value was valid ajFalse if it was bad and was "corrected"

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagAdd

Synopsis

Prototype

AjBool ajFeatTagAdd (
      AjPFeature thys,
      const AjPStr tag,
      const AjPStr value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const AjPStr	tag	Input	Feature tag
const AjPStr	value	Input	Feature tag value
AjBool		RETURN	ajTrue if value was valid ajFalse if it was bad and was "corrected"

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableNew

Synopsis

Prototype

AjPFeattable ajFeattableNew (
      const AjPStr name 
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	Name for new feature table (or NULL for unnamed)
AjPFeattable		RETURN	Pointer to a new (empty) feature table

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatUfoRead

Synopsis

Prototype

AjPFeattable ajFeatUfoRead (
      AjPFeattabIn featin,
      const AjPStr ufo
);

Type	Name	Read/Write	Description
AjPFeattabIn	featin	Modify	Feature input object
const AjPStr	ufo	Input	UFO feature spec
AjPFeattable		RETURN	Feature table created, (or NULL if failed)

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableSetLength

This is needed to reverse the table correctly

Synopsis

Prototype

void ajFeattableSetLength (
      AjPFeattable thys,
      ajuint len
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table object
ajuint	len	Input	Length
void		RETURN

Input

Input & Output

Returns

Description

This is needed to reverse the table correctly

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableSetNuc

Synopsis

Prototype

void ajFeattableSetNuc (
      AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table object
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableSetProt

Synopsis

Prototype

void ajFeattableSetProt (
      AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table object
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableReverse

Synopsis

Prototype

void ajFeattableReverse (
      AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table object
void		RETURN

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatReverse

Synopsis

Prototype

void ajFeatReverse (
      AjPFeature thys,
      ajint ilen
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature object
ajint	ilen	Input	Sequence length
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableSetRange

Synopsis

Prototype

void ajFeattableSetRange (
      AjPFeattable thys,
      ajint fbegin,
      ajint fend
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table object
ajint	fbegin	Input	Begin position
ajint	fend	Input	End position
void		RETURN

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableNewDna

Synopsis

Prototype

AjPFeattable ajFeattableNewDna (
      const AjPStr name
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	Name for new feature table (or NULL for unnamed)
AjPFeattable		RETURN	Pointer to a new (empty) feature table

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableNewSeq

Synopsis

Prototype

AjPFeattable ajFeattableNewSeq (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object to provide the name and type
AjPFeattable		RETURN	Pointer to a new (empty) feature table

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableNewProt

Synopsis

Prototype

AjPFeattable ajFeattableNewProt (
      const AjPStr name
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	Name for new feature table (or NULL for unnamed)
AjPFeattable		RETURN	Pointer to a new (empty) feature table

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableCopy

For cases where we need a copy we can safely change and/or delete.

Synopsis

Prototype

AjPFeattable ajFeattableCopy (
      const AjPFeattable orig
);

Type	Name	Read/Write	Description
const AjPFeattable	orig	Input	Original feature table
AjPFeattable		RETURN	Feature table copy of the original

Input

Returns

Description

For cases where we need a copy we can safely change and/or delete.

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableCopyLimit

For cases where we need a copy we can safely change and/or delete.

Synopsis

Prototype

AjPFeattable ajFeattableCopyLimit (
      const AjPFeattable orig,
      ajint limit
);

Type	Name	Read/Write	Description
const AjPFeattable	orig	Input	Original feature table
ajint	limit	Input	Limit to number of features copied
AjPFeattable		RETURN	Feature table copy of the original

Input

Returns

Description

For cases where we need a copy we can safely change and/or delete.

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatCopy

For cases where we need a copy we can safely change and/or delete.

Synopsis

Prototype

AjPFeature ajFeatCopy (
      const AjPFeature orig
);

Type	Name	Read/Write	Description
const AjPFeature	orig	Input	Original feature
AjPFeature		RETURN	Feature copy of the original

Input

Returns

Description

For cases where we need a copy we can safely change and/or delete.

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTrace

Synopsis

Prototype

void ajFeatTrace (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
void		RETURN

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagTrace

Synopsis

Prototype

void ajFeatTagTrace (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
void		RETURN

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagIter

Synopsis

Prototype

AjIList ajFeatTagIter (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
AjIList		RETURN	List iterator

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTagval

Synopsis

Prototype

AjBool ajFeatTagval (
      AjIList iter,
      AjPStr* tagnam,
      AjPStr* tagval
);

Type	Name	Read/Write	Description
AjIList	iter	Modify	List iterator from ajFeatTagIter
AjPStr*	tagnam	Output	Tag name
AjPStr*	tagval	Output	Tag val
AjBool		RETURN	ajTrue if another tag-value pair was returned

Output

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeattableTrace

Synopsis

Prototype

void ajFeattableTrace (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
void		RETURN

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTypeNuc

Synopsis

Prototype

const AjPStr ajFeatTypeNuc (
      const AjPStr type
);

Type	Name	Read/Write	Description
const AjPStr	type	Input	Type name
const AjPStr		RETURN	Valid feature type

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTypeProt

Synopsis

Prototype

const AjPStr ajFeatTypeProt (
      const AjPStr type
);

Type	Name	Read/Write	Description
const AjPStr	type	Input	Type name
const AjPStr		RETURN	Valid feature type

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatExit

Cleans up feature table internal memory

Synopsis

Prototype

void ajFeatExit (
      void
);

Type	Name	Read/Write	Description
void		RETURN

Returns

Description

Cleans up feature table internal memory

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatUnused

Synopsis

Prototype

void ajFeatUnused (
      void
);

Type	Name	Read/Write	Description
void		RETURN

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTypeIsCds

Synopsis

Prototype

AjBool ajFeatTypeIsCds (
      const AjPFeature gf
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
AjBool		RETURN	ajTrue on success

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function ajFeatTypeMatchC

Synopsis

Prototype

AjBool ajFeatTypeMatchC (
      const AjPFeature gf,
      const char* txt
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
const char*	txt	Input	Feature type name to test
AjBool		RETURN	ajTrue on success

Input

Returns

Description

Usage

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Function ajFeatTypeMatchS

Synopsis

Prototype

AjBool ajFeatTypeMatchS (
      const AjPFeature gf,
      const AjPStr str
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
const AjPStr	str	Input	Feature type name to test
AjBool		RETURN	ajTrue on success

Input

Returns

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Function ajFeatIsLocal

Synopsis

Prototype

AjBool ajFeatIsLocal (
      const AjPFeature gf
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
AjBool		RETURN	ajTrue on success

Input

Returns

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Function ajFeatIsLocalRange

Synopsis

Prototype

AjBool ajFeatIsLocalRange (
      const AjPFeature gf,
      ajuint start,
      ajuint end
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
ajuint	start	Input	start of range
ajuint	end	Input	end of range
AjBool		RETURN	ajTrue on success

Input

Returns

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Function ajFeatIsChild

Synopsis

Prototype

AjBool ajFeatIsChild (
      const AjPFeature gf
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
AjBool		RETURN	Returns AJTRUE if it is a child, AJFALSE if it is not a child

Input

Returns

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Function ajFeatIsMultiple

Synopsis

Prototype

AjBool ajFeatIsMultiple (
      const AjPFeature gf
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
AjBool		RETURN	Returns AJTRUE if it is a member

Input

Returns

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Function ajFeatIsCompMult

Synopsis

Prototype

AjBool ajFeatIsCompMult (
      const AjPFeature gf
);

Type	Name	Read/Write	Description
const AjPFeature	gf	Input	Feature
AjBool		RETURN	Returns AJTRUE if it is a complemented multiple

Input

Returns

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Function ajFeattabOutClear

Synopsis

Prototype

void ajFeattabOutClear (
      AjPFeattabOut* thys
);

Type	Name	Read/Write	Description
AjPFeattabOut*	thys	Delete	feature format
void		RETURN	Feature table output object

Output

Returns

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Function ajFeattabOutDel

Synopsis

Prototype

void ajFeattabOutDel (
      AjPFeattabOut* thys
);

Type	Name	Read/Write	Description
AjPFeattabOut*	thys	Delete	feature format
void		RETURN	Feature table output object

Output

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Function ajFeattablePos

For strings, the result can go off the end to the terminating NULL. For sequences the maximum is the last base.

Synopsis

Prototype

ajuint ajFeattablePos (
      const AjPFeattable thys,
      ajint ipos
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Target feature table.
ajint	ipos	Input	Position.
ajuint		RETURN	string position between 1 and length.

Input

Returns

Description

For strings, the result can go off the end to the terminating NULL. For sequences the maximum is the last base.

Usage

Example

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Function ajFeattablePosI

imin is a minimum relative position, also counted from the end if negative. Usually this is the start position when the end of a range is being tested.

Synopsis

Prototype

ajuint ajFeattablePosI (
      const AjPFeattable thys,
      ajuint imin,
      ajint ipos
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Target feature table.
ajuint	imin	Input	Start position.
ajint	ipos	Input	Position.
ajuint		RETURN	string position between 1 and length.

Input

Returns

Description

imin is a minimum relative position, also counted from the end if negative. Usually this is the start position when the end of a range is being tested.

Usage

Example

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Function ajFeattablePosII

imin is a minimum relative position, also counted from the end if negative. Usually this is the start position when the end of a range is being tested.

For strings, the result can go off the end to the terminating NULL. For sequences the maximum is the last base.

Synopsis

Prototype

ajuint ajFeattablePosII (
      ajuint ilen,
      ajuint imin,
      ajint ipos
);

Type	Name	Read/Write	Description
ajuint	ilen	Input	maximum length.
ajuint	imin	Input	Start position.
ajint	ipos	Input	Position.
ajuint		RETURN	string position between 1 and length.

Input

Returns

Description

imin is a minimum relative position, also counted from the end if negative. Usually this is the start position when the end of a range is being tested.

For strings, the result can go off the end to the terminating NULL. For sequences the maximum is the last base.

Usage

Example

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Function ajFeattableTrimOff

Called where a sequence has been trimmed, so we have to allow for missing sequence positions at the start (ioffset) or at the end (ilen).

Synopsis

Prototype

AjBool ajFeattableTrimOff (
      AjPFeattable thys,
      ajuint ioffset,
      ajuint ilen
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Target feature table.
ajuint	ioffset	Input	Offset from start of sequence
ajuint	ilen	Input	Length of sequence
AjBool		RETURN	AjTrue returned if successful.

Input

Input & Output

Returns

Description

Called where a sequence has been trimmed, so we have to allow for missing sequence positions at the start (ioffset) or at the end (ilen).

Usage

Example

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Function ajFeatTrimOffRange

Called where a sequence has been trimmed, so we have to allow for missing sequence positions at the start (ioffset) or at the end (ilen).

Synopsis

Prototype

AjBool ajFeatTrimOffRange (
      AjPFeature ft,
      ajuint ioffset,
      ajuint begin,
      ajuint end,
      AjBool dobegin,
      AjBool doend
);

Type	Name	Read/Write	Description
AjPFeature	ft	Modify	Target feature
ajuint	ioffset	Input	Offset from start of sequence
ajuint	begin	Input	Range start of sequence
ajuint	end	Input	range end of sequence
AjBool	dobegin	Input	Reset begin
AjBool	doend	Input	Reset end
AjBool		RETURN	AjTrue returned if successful.

Input

Input & Output

Returns

Description

Called where a sequence has been trimmed, so we have to allow for missing sequence positions at the start (ioffset) or at the end (ilen).

Usage

Example

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Function ajFeatDefName

Synopsis

Prototype

void ajFeatDefName (
      AjPFeattable thys,
      const AjPStr setname
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Output	Feature table
const AjPStr	setname	Input	Name set by caller
void		RETURN

Input

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Function ajFeattableWriteDebug

Synopsis

Prototype

AjBool ajFeattableWriteDebug (
      AjPFeattabOut ftout,
      const AjPFeattable ftable
);

Type	Name	Read/Write	Description
AjPFeattabOut	ftout	Modify	Feature table output object
const AjPFeattable	ftable	Input	Feature table
AjBool		RETURN	Always true

Input

Input & Output

Returns

Description

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Example

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Function ajFeattablePrint

Synopsis

Prototype

AjBool ajFeattablePrint (
      const AjPFeattable ftable,
      AjPFile outf
);

Type	Name	Read/Write	Description
const AjPFeattable	ftable	Input	Feature table
AjPFile	outf	Modify	Output file object
AjBool		RETURN	Always true

Input

Input & Output

Returns

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Example

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Function ajFeatPrintFormat

Synopsis

Prototype

void ajFeatPrintFormat (
      AjPFile outf,
      AjBool full
);

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

Input

Input & Output

Returns

Description

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Example

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Function ajFeattagIsNote

Synopsis

Prototype

AjBool ajFeattagIsNote (
      const AjPStr tag
);

Type	Name	Read/Write	Description
const AjPStr	tag	Input	Feature tag
AjBool		RETURN	ajTrue on success

Input

Returns

Description

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Example

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