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:

ajFeatNew	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewBetween	Simple constructor with location between the start positions and the previous base.
ajFeatNewSub	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewII	Simple constructor with only start and end positions
ajFeatNewIISub	Simple constructor with only start and end positions
ajFeatNewIIRev	Simple constructor with only start and end positions, sets feature to be on the reverse strand
ajFeatNewIIRevSub	Simple constructor with only start and end positions, sets feature to be on the reverse strand
ajFeatNewProt	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewProtSub	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewProtFlags	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewProtFlagsSub	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatCompByStart	Compare two features by their start.
ajFeatCompByEnd	Compare two features by their end.
ajFeatCompByGroup	Compare two features by their group and exon numbers
ajFeatCompByType	Compare two features by their type (key).
ajFeatNewNuc	Constructor for a new feature, automatically added to the specified table.
ajFeatNewNucSub	Constructor for a new feature, automatically added to the specified table.
ajFeatNewNucFlags	Constructor for a new feature, automatically added to the specified table.
ajFeatNewNucFlagsSub	Constructor for a new feature, automatically added to the specified table.

Function ajFeatNew

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

From EMBOSS 2.0.0

Function ajFeatNewBetween

Prototype

AjPFeature ajFeatNewBetween (
      AjPFeattable thys,
      ajint Start
);

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
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.5.0

Function ajFeatNewSub

Prototype

AjPFeature ajFeatNewSub (
      AjPFeattable thys,
      AjPFeature parent,
      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
AjPFeature	parent	Modify	Parent 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

From EMBOSS 6.4.0

Function ajFeatNewII

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

From EMBOSS 2.1.0

Function ajFeatNewIISub

Prototype

AjPFeature ajFeatNewIISub (
      AjPFeattable thys,
      AjPFeature parent,
      ajint Start,
      ajint End
);

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

From EMBOSS 6.4.0

Function ajFeatNewIIRev

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

From EMBOSS 2.8.0

Function ajFeatNewIIRevSub

Prototype

AjPFeature ajFeatNewIIRevSub (
      AjPFeattable thys,
      AjPFeature parent,
      ajint Start,
      ajint End
);

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

From EMBOSS 6.4.0

Function ajFeatNewProt

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

From EMBOSS 2.0.0

Function ajFeatNewProtSub

Prototype

AjPFeature ajFeatNewProtSub (
      AjPFeattable thys,
      AjPFeature parent,
      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
AjPFeature	parent	Modify	Parent 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

From EMBOSS 6.4.0

Function ajFeatNewProtFlags

Prototype

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

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
ajuint	flags	Input	flags.
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.4.0

Function ajFeatNewProtFlagsSub

Prototype

AjPFeature ajFeatNewProtFlagsSub (
      AjPFeattable thys,
      AjPFeature parent,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score,
      ajuint flags
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
AjPFeature	parent	Modify	Parent 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
ajuint	flags	Input	flags.
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.4.0

Function ajFeatCompByStart

Prototype

ajint ajFeatCompByStart (
      const void* a,
      const void* b
);

Type	Name	Read/Write	Description
const void*	a	Input	feature
const void*	b	Input	another feature
ajint		RETURN	-1 if a is less than b, 0 if a is equal to b else +1.

From EMBOSS 6.4.0

Function ajFeatCompByEnd

Prototype

ajint ajFeatCompByEnd (
      const void* a,
      const void* b
);

Type	Name	Read/Write	Description
const void*	a	Input	feature
const void*	b	Input	another feature
ajint		RETURN	-1 if a is less than b, 0 if a is equal to b else +1.

From EMBOSS 6.4.0

Function ajFeatCompByGroup

Prototype

ajint ajFeatCompByGroup (
      const void* a,
      const void* b
);

Type	Name	Read/Write	Description
const void*	a	Input	feature
const void*	b	Input	another feature
ajint		RETURN	-1 if a is less than b, 0 if a is equal to b else +1.

From EMBOSS 6.4.0

Function ajFeatCompByType

Prototype

ajint ajFeatCompByType (
      const void* a,
      const void* b
);

Type	Name	Read/Write	Description
const void*	a	Input	feature
const void*	b	Input	another feature
ajint		RETURN	-1 if a is less than b, 0 if a is equal to b else +1.

From EMBOSS 6.4.0

Function ajFeatNewNuc

Prototype

AjPFeature ajFeatNewNuc (
      AjPFeattable thys,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score,
      char strand,
      ajint frame,
      ajint exon,
      ajint Start2,
      ajint End2,
      const AjPStr entryid,
      const AjPStr label
);

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
ajint	exon	Input	exon number (0 for default value)
ajint	Start2	Input	2nd Start position of the feature
ajint	End2	Input	2nd End position of the feature
const AjPStr	entryid	Input	Entry ID for location in another entry
const AjPStr	label	Input	Label for location (non-numeric)
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.4.0

Function ajFeatNewNucSub

Prototype

AjPFeature ajFeatNewNucSub (
      AjPFeattable thys,
      AjPFeature parent,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score,
      char strand,
      ajint frame,
      ajint exon,
      ajint Start2,
      ajint End2,
      const AjPStr entryid,
      const AjPStr label
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
AjPFeature	parent	Modify	Parent 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
ajint	exon	Input	exon number (0 for default value)
ajint	Start2	Input	2nd Start position of the feature
ajint	End2	Input	2nd End position of the feature
const AjPStr	entryid	Input	Entry ID for location in another entry
const AjPStr	label	Input	Label for location (non-numeric)
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.4.0

Function ajFeatNewNucFlags

Prototype

AjPFeature ajFeatNewNucFlags (
      AjPFeattable thys,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score,
      char strand,
      ajint frame,
      ajint exon,
      ajint Start2,
      ajint End2,
      const AjPStr entryid,
      const AjPStr label,
      ajuint flags
);

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
ajint	exon	Input	exon number (0 for default value)
ajint	Start2	Input	2nd Start position of the feature
ajint	End2	Input	2nd End position of the feature
const AjPStr	entryid	Input	Entry ID for location in another entry
const AjPStr	label	Input	Label for location (non-numeric)
ajuint	flags	Input	flags.
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.4.0

Function ajFeatNewNucFlagsSub

Prototype

AjPFeature ajFeatNewNucFlagsSub (
      AjPFeattable thys,
      AjPFeature parent,
      const AjPStr source,
      const AjPStr type,
      ajint Start,
      ajint End,
      float score,
      char strand,
      ajint frame,
      ajint exon,
      ajint Start2,
      ajint End2,
      const AjPStr entryid,
      const AjPStr label,
      ajuint flags
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Pointer to the ajFeattable which will own the feature
AjPFeature	parent	Modify	Parent 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
ajint	exon	Input	exon number (0 for default value)
ajint	Start2	Input	2nd Start position of the feature
ajint	End2	Input	2nd End position of the feature
const AjPStr	entryid	Input	Entry ID for location in another entry
const AjPStr	label	Input	Label for location (non-numeric)
ajuint	flags	Input	flags.
AjPFeature		RETURN	newly allocated feature object

From EMBOSS 6.4.0

Section: Feature Object Destructors

No reference counting (for now).

Functions:

ajFeattableDel	Destructor for ajFeattable objects. If the given object (pointer) is NULL, or a NULL pointer, simply returns.
ajFeatDel	Destructor for AjPFeature objects. If the given object (pointer) is NULL, or a NULL pointer, simply returns.

Function ajFeattableDel

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

From EMBOSS 2.1.0

Function ajFeatDel

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

From EMBOSS 1.0.0

Section: Feature Assignments

Functions:

ajFeatSortByType	Sort Feature table by Type.
ajFeatSortByStart	Sort Feature table by Start position.
ajFeatSortByEnd	Sort Feature table by End position.

Function ajFeatSortByType

Prototype

void ajFeatSortByType (
      AjPFeattable Feattab
);

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

From EMBOSS 1.0.0

Function ajFeatSortByStart

Prototype

void ajFeatSortByStart (
      AjPFeattable Feattab
);

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

From EMBOSS 1.0.0

Function ajFeatSortByEnd

Prototype

void ajFeatSortByEnd (
      AjPFeattable Feattab
);

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

From EMBOSS 1.0.0

Section: Feature Table Modifiers

Functions:

ajFeattableAdd	Method to add a new AjPFeature to a AjPFeattable
ajFeattableAddNew	Method to add a new AjPFeature to a AjPFeattable as a new feature, updating the feature group.
ajFeattableMerge	Merges a feature table into an existing feature table.

Function ajFeattableAdd

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

From EMBOSS 2.1.0

Function ajFeattableAddNew

Prototype

void ajFeattableAddNew (
      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

From EMBOSS 2.1.0

Function ajFeattableMerge

Prototype

ajuint ajFeattableMerge (
      AjPFeattable thys,
      const AjPFeattable srctable
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table to be appended to
const AjPFeattable	srctable	Input	Additional feature table
ajuint		RETURN	Size of the new feature table.

From EMBOSS 6.5.0

Section: Feature Object Operators

Functions:

ajFeattableClear	Clears a feature table of all features
ajFeatTypeGetCategory	returns the category name for a feature type
ajFeattableGetEntry	Return the full text
ajFeattableGetQryC	Returns the query string of a feature table data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajFeattableGetQryS	Returns the query string of a feature table data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajFeattableGetTypeC	Returns the name of a feature table object. This is a copy of the pointer to the name, and is still owned by the feature table and is not to be destroyed.
ajFeattableGetTypeS	Returns the name of a feature table object. This is a copy of the pointer to the name, and is still owned by the feature table and is not to be destroyed.
ajFeattableGetXrefs	Returns all cross-references from a feature table
ajFeatframeGetFrame	Converts a frame number in the range 0 to 3 to a GFF frame character or '.' as the general default
ajFeatframeGetFrameNuc	Converts a frame number in the range 0 to 3 to a GFF frame character or '0' for the nucleotide default
ajFeatstrandGetStrand	Converts a strand number to a GFF strand character. NULL characters are converted to '+' All other values are simply cast to character.
ajFeattableIsCircular	Returns true if a feature table is circular
ajFeattableIsNuc	Returns ajTrue if a feature table is nucleotide
ajFeattableIsProt	Returns ajTrue if a feature table is protein
ajFeattableGetBegin	Returns the feature table start position, or 1 if no start has been set.
ajFeattableGetEnd	Returns the features table end position, or the feature table length if no end has been set.
ajFeattableGetLen	Returns the sequence length of a feature table
ajFeattableGetName	Returns the name of a feature table object. This is a copy of the pointer to the name, and is still owned by the feature table and is not to be destroyed.
ajFeattableGetSize	Returns the size of a feature table object.
ajFeattableGetScorerange	Returns the range of scores for feature table object.
ajFeatGetScorerange	Returns the range of scores for a feature object.
ajFeatGetFlags	Returns the sequence matching a feature. For multiple location features (joins in an EMBL/GenBank feature table) the full feature table is used to find all exons.
ajFeatGetSeq	Returns the sequence matching a feature.
ajFeatGetSeqJoin	Returns the sequence matching a feature. For multiple location features (joins in an EMBL/GenBank feature table) the full feature table is used to find all exons.
ajFeatGetRemoteseq	Returns a sequence entry from a feature location which points to another entry
ajFeatGetSubtype	Returns the feature type of the first subfeature
ajFeatGetXrefs	Returns all cross-references from a feature
ajFeatLocMark	Returns a sequence entry converted to lower case where a feature location matches.
ajFeatGetNoteC	Finds a named note tag (with a * prefix)
ajFeatGetNoteCI	Finds a named note tag (with a * prefix)
ajFeatGetNoteSI	Finds a named note tag (with a * prefix)
ajFeatGetNoteS	Finds a named note tag (with a * prefix)
ajFeatGetTagC	Returns the nth value of a named feature tag.
ajFeatGetTagS	Returns the nth value of a named feature tag.
ajFeatGetType	Returns the type (key) of a feature object. This is a copy of the pointer to the type, and is still owned by the feature and is not to be destroyed.
ajFeatGetSource	Returns the source name of a feature object.
ajFeatGetStart	Returns the start position of a feature object.
ajFeatGetStrand	Returns the strand of a feature object.
ajFeatGetEnd	Returns the end position of a feature object.
ajFeatGetLength	Returns the sequence length of a feature object.
ajFeatGetScore	Returns the score of a feature object.
ajFeatGetForward	Returns the direction of a feature object.
ajFeatGetFrame	Returns the reading frame of a feature object.
ajFeatGetTranslation	Returns translation tag value
ajFeatTest	Temporary testing function for feature handling to be deleted when all is working happily
ajFeatVocabGetTags	Returns tags table for a named feature format
ajFeatVocabGetTagsNuc	Returns tags table for a named nucleotide feature format
ajFeatVocabGetTagsProt	Returns tags table for a named protein feature format
ajFeatVocabGetTypes	Returns types table for a named feature format
ajFeatVocabGetTypesNuc	Returns types table for a named nucleotide feature format
ajFeatVocabGetTypesProt	Returns types table for a named protein feature format
ajFeatVocabInit	Initialises feature table internals for a named feature format
ajFeatVocabInitNuc	Initialises feature table internals for a named feature format
ajFeatVocabInitProt	Initialises feature table internals for a named feature format
ajFeatSetDescApp	Sets the description for a feature
ajFeatSetDesc	Sets the description for a feature
ajFeatSetSource	Sets the source for a feature
ajFeatSetScore	Sets the score for a feature
ajFeatSetStrand	Sets the strand for a feature
ajFeatTagSetC	Sets a feature tag value
ajFeatTagSet	Sets a feature tag value
ajFeattagSpecialGff2	Special processing for known GFF tags
ajFeattagSpecialGff3	Special processing for known GFF3 tags
ajFeatTagAddCC	Sets a feature tag value, creating a new feature tag even if one already exists.
ajFeatTagAddCS	Sets a feature tag value, creating a new feature tag even if one already exists.
ajFeatTagAddSS	Sets a feature tag value, creating a new feature tag even if one already exists.
ajFeatTagAddTag	Sets a feature tag value, creating a new feature tag even if one already exists.
ajFeattagSpecial	Special processing for known internal (EMBL) tags
ajFeattableNew	Constructor for a new (generic) feature table. Does not define the feature table type.
ajFeattableReset	Resets a feature table with a new name
ajFeattableSetCircular	Sets a feature table to be circular
ajFeattableSetDefname	Provides a unique (for this program run) name for a feature table.
ajFeattableSetLength	Sets the length of a feature table with the length of the source sequence.
ajFeattableSetLinear	Sets a feature table to be linear
ajFeattableSetNuc	Sets the type of a feature table as nucleotide
ajFeattableSetProt	Sets the type of a feature table as Protein
ajFeattableSetRange	Set the begin and end range for a feature table
ajFeattableSetReverse	Sets a feature table to be reversed
ajFeattableReverse	Reverse the features in a feature table by iterating through and reversing all positions and strands.
ajFeatReverse	Reverse one feature by reversing all positions and strand.
ajFeattableNewDna	Constructor for a new DNA feature table
ajFeattableNewSeq	Constructor for a new feature table for an existing sequence. The feature table type is determined by the sequence type.
ajFeattableNewProt	Constructor for a new protein feature table
ajFeatGfftagAddCS	Constructor for a feature GFF3 tag-value pair
ajFeatGfftagAddSS	Constructor for a feature GFF3 tag-value pair
ajFeatGfftagAddTag	Sets a feature tag value, creating a new feature tag even if one already exists.
ajFeattableNewFtable	Makes a copy of a feature table.
ajFeattableNewFtableLimit	Makes a copy of a feature table using only a limited number of features.
ajFeatNewFeat	Makes a copy of a feature.
ajFeatTrace	Traces (to the debug file) a feature object
ajFeatTagTrace	Traces (to the debug file) the tag-value pairs of a feature object
ajFeatGfftagTrace	Traces (to the debug file) the GFF tag-value pairs of a feature object
ajFeatGfftagsNew	Creates a structure holding GFF tag value pairs
ajFeatGfftagsDel	Destroys a structure holding GFF tag value pairs
ajFeatGetGfftags	Returns an object with all feature GFF tag-value pairs
ajFeatGetId	Returns the GFF ID tag of a feature with GFF tag-value pairs
ajFeatGetParent	Returns the GFF Parent tag of a feature with GFF tag-value pairs
ajFeatTagIter	Returns an iterator over all feature tag-value pairs
ajFeatSubIter	Returns an iterator over all subfeaturers
ajFeatTagval	Returns the tag-value pairs of a feature object
ajFeattableTrace	Traces (to the debug file) a complete feature table
ajFeatTypeNuc	Given a feature type name, returns the valid feature type for the internal DNA feature table
ajFeatTypeProt	Given a feature type name, returns the valid feature type for the internal protein feature table
ajFeattypeGetExternal	Given a feature type name, returns the valid feature type for a feature table
ajFeattypeGetInternal	Given a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalEmbl	Given a feature type name, returns the valid feature type for an EMBL format feature table
ajFeattypeGetInternalNuc	Given a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalPir	Given a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalProt	Given a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalRefseqp	Given a feature type name, returns the valid feature type for a REFSEQP format feature table
ajFeattagGetNameC	Given a feature tag name, returns the valid feature tag name for a feature table
ajFeattagGetNameS	Given a feature tag name, returns the valid feature tag name for a feature table
ajFeattagFormat	Converts a feature tag value into the correct format, after checking it is an acceptable value
ajFeattagGetLimit	Returns the controlled vocabulary list for a limited value.
ajFeatUnused	Dummy function to prevent compiler warnings
ajFeatTypeIsCds	Tests whether the feature is a CDS feature
ajFeatTypeMatchC	Tests whether the feature type matches a given string including testing for alternative names
ajFeatTypeMatchS	Tests whether the feature type matches a given string including testing for alternative names
ajFeatTypeMatchWildS	Tests whether the feature type matches a given wildcard string including testing for alternative names
ajFeatIsLocal	Tests whether the feature is local to the sequence. Returns AJTRUE if it is local, AJFALSE if remote.
ajFeatIsLocalRange	Tests whether the feature is local and in the specified range of the sequence. Returns AJTRUE if it is local and within the range. (Any label location is assumed to be outside the range.)
ajFeatIsMultiple	Tests whether the feature is a member of a join, group order or one_of
ajFeatIsCompMult	Tests whether the feature is a member of a complement around a multiple (join, etc.)
ajFeattablePos	Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.
ajFeattablePosI	Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.
ajFeattablePosII	Converts a position into a true position. If ipos is negative, it is counted from the end of the sequence rather than the beginning.
ajFeattableTrimOff	Trim a feature table using the Begin and Ends.
ajFeattableTrim	Trim a feature table using the Begin and Ends.
ajFeatTrimOffRange	Trim a feature table using the Begin and Ends.
ajFeattagIsNote	Tests whether the feature tag is a note (the default feature tag)
ajFeatExit	Cleans up feature table internal memory
ajFeatWarn	Formatted write as a warning message.

Function ajFeattableClear

Prototype

void ajFeattableClear (
      AjPFeattable thys
);

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

From EMBOSS 2.1.0

Function ajFeatTypeGetCategory

Prototype

const AjPStr ajFeatTypeGetCategory (
      const AjPStr type
);

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

From EMBOSS 6.1.0

Function ajFeattableGetEntry

Prototype

const AjPStr ajFeattableGetEntry (
      const AjPFeattable thys
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table object
const AjPStr		RETURN	Returned full text

From EMBOSS 6.4.0

Function ajFeattableGetQryC

Prototype

const char* ajFeattableGetQryC (
      const AjPFeattable ftable
);

Type	Name	Read/Write	Description
const AjPFeattable	ftable	Input	Feature table data object.
const char*		RETURN	Query as a character string.

From EMBOSS 6.4.0

Function ajFeattableGetQryS

Prototype

const AjPStr ajFeattableGetQryS (
      const AjPFeattable ftable
);

Type	Name	Read/Write	Description
const AjPFeattable	ftable	Input	Feature table data object.
const AjPStr		RETURN	Query as a string.

From EMBOSS 6.4.0

Function ajFeattableGetTypeC

Prototype

const char* ajFeattableGetTypeC (
      const AjPFeattable thys
);

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

From EMBOSS 4.0.0

Function ajFeattableGetTypeS

Prototype

const AjPStr ajFeattableGetTypeS (
      const AjPFeattable thys
);

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

From EMBOSS 4.0.0

Function ajFeattableGetXrefs

Prototype

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

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

From EMBOSS 6.1.0

Function ajFeatframeGetFrame

Prototype

char ajFeatframeGetFrame (
      ajint frame
);

Type	Name	Read/Write	Description
ajint	frame	Input	Feature frame number
char		RETURN	character for this frame in GFF

From EMBOSS 6.4.0

Function ajFeatframeGetFrameNuc

Prototype

char ajFeatframeGetFrameNuc (
      ajint frame
);

Type	Name	Read/Write	Description
ajint	frame	Input	Feature frame number
char		RETURN	character for this frame in GFF

From EMBOSS 6.4.0

Function ajFeatstrandGetStrand

Prototype

char ajFeatstrandGetStrand (
      ajint strand
);

Type	Name	Read/Write	Description
ajint	strand	Input	Strand
char		RETURN	GFF character for this strand.

From EMBOSS 6.4.0

Function ajFeattableIsCircular

Prototype

AjBool ajFeattableIsCircular (
      const AjPFeattable thys
);

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

From EMBOSS 2.5.0

Function ajFeattableIsNuc

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

From EMBOSS 2.5.0

Function ajFeattableIsProt

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

From EMBOSS 2.5.0

Function ajFeattableGetBegin

Prototype

ajint ajFeattableGetBegin (
      const AjPFeattable thys
);

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

From EMBOSS 6.2.0

Function ajFeattableGetEnd

Prototype

ajint ajFeattableGetEnd (
      const AjPFeattable thys
);

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

From EMBOSS 6.2.0

Function ajFeattableGetLen

Prototype

ajint ajFeattableGetLen (
      const AjPFeattable thys
);

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

From EMBOSS 6.2.0

Function ajFeattableGetName

Prototype

const AjPStr ajFeattableGetName (
      const AjPFeattable thys
);

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

From EMBOSS 2.1.0

Function ajFeattableGetSize

Prototype

ajuint ajFeattableGetSize (
      const AjPFeattable thys
);

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

From EMBOSS 6.1.0

Function ajFeattableGetScorerange

Prototype

AjBool ajFeattableGetScorerange (
      const AjPFeattable thys,
      float* minscore,
      float* maxscore
);

Type	Name	Read/Write	Description
const AjPFeattable	thys	Input	Feature table
float*	minscore	Output	Minimum score
float*	maxscore	Output	Maximum score
AjBool		RETURN	True if scores were found

From EMBOSS 6.5.0

Function ajFeatGetScorerange

Prototype

AjBool ajFeatGetScorerange (
      const AjPFeature thys,
      float* minscore,
      float* maxscore
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
float*	minscore	Output	Minimum score
float*	maxscore	Output	Maximum score
AjBool		RETURN	True if scores were found

From EMBOSS 6.5.0

Function ajFeatGetFlags

Prototype

AjBool ajFeatGetFlags (
      const AjPFeature thys,
      AjPStr* Pflagstr
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
AjPStr*	Pflagstr	Modify	Sequence for this feature
AjBool		RETURN	True on success

From EMBOSS 6.2.0

Function ajFeatGetSeq

Prototype

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

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

From EMBOSS 6.1.0

Function ajFeatGetSeqJoin

Prototype

AjBool ajFeatGetSeqJoin (
      const AjPFeature thys,
      const AjPSeq seq,
      AjPStr* Pseqstr
);

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

From EMBOSS 6.2.0

Function ajFeatGetRemoteseq

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

From EMBOSS 6.1.0

Function ajFeatGetSubtype

Prototype

const AjPStr ajFeatGetSubtype (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
const AjPStr		RETURN	Subfeature type

From EMBOSS 6.5.0

Function ajFeatGetXrefs

Prototype

AjBool ajFeatGetXrefs (
      const AjPFeature thys,
      AjPList* Pxreflist
);

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

From EMBOSS 6.1.0

Function ajFeatLocMark

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

From EMBOSS 4.1.0

Function ajFeatGetNoteC

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)

From EMBOSS 4.0.0

Function ajFeatGetNoteCI

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)

From EMBOSS 4.0.0

Function ajFeatGetNoteSI

Prototype

AjBool ajFeatGetNoteSI (
      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)

From EMBOSS 6.2.0

Function ajFeatGetNoteS

Prototype

AjBool ajFeatGetNoteS (
      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)

From EMBOSS 6.2.0

Function ajFeatGetTagC

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)

From EMBOSS 6.1.0

Function ajFeatGetTagS

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)

From EMBOSS 6.1.0

Function ajFeatGetType

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

From EMBOSS 2.1.0

Function ajFeatGetSource

Prototype

const AjPStr ajFeatGetSource (
      const AjPFeature thys
);

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

From EMBOSS 4.0.0

Function ajFeatGetStart

Prototype

ajuint ajFeatGetStart (
      const AjPFeature thys
);

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

From EMBOSS 2.1.0

Function ajFeatGetStrand

Prototype

char ajFeatGetStrand (
      const AjPFeature thys
);

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

From EMBOSS 4.0.0

Function ajFeatGetEnd

Prototype

ajuint ajFeatGetEnd (
      const AjPFeature thys
);

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

From EMBOSS 2.1.0

Function ajFeatGetLength

Prototype

ajuint ajFeatGetLength (
      const AjPFeature thys
);

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

From EMBOSS 4.0.0

Function ajFeatGetScore

Prototype

float ajFeatGetScore (
      const AjPFeature thys
);

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

From EMBOSS 4.0.0

Function ajFeatGetForward

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

From EMBOSS 2.1.0

Function ajFeatGetFrame

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)

From EMBOSS 2.1.0

Function ajFeatGetTranslation

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

From EMBOSS 6.1.0

Function ajFeatTest

Prototype

void ajFeatTest (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 2.0.0

Function ajFeatVocabGetTags

Prototype

const AjPTable ajFeatVocabGetTags (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Tags table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabGetTagsNuc

Prototype

const AjPTable ajFeatVocabGetTagsNuc (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Tags table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabGetTagsProt

Prototype

const AjPTable ajFeatVocabGetTagsProt (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Tags table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabGetTypes

Prototype

const AjPTable ajFeatVocabGetTypes (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Type table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabGetTypesNuc

Prototype

const AjPTable ajFeatVocabGetTypesNuc (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Type table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabGetTypesProt

Prototype

const AjPTable ajFeatVocabGetTypesProt (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Type table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabInit

Prototype

const AjPTable ajFeatVocabInit (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Type table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabInitNuc

Prototype

const AjPTable ajFeatVocabInitNuc (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Type table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatVocabInitProt

Prototype

const AjPTable ajFeatVocabInitProt (
      const char* name
);

Type	Name	Read/Write	Description
const char*	name	Input	Feature format name
const AjPTable		RETURN	Type table on success NULL on failure

From EMBOSS 6.4.0

Function ajFeatSetDescApp

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

From EMBOSS 2.3.0

Function ajFeatSetDesc

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

From EMBOSS 2.0.0

Function ajFeatSetSource

Prototype

void ajFeatSetSource (
      AjPFeature thys,
      const AjPStr source
);

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

From EMBOSS 6.4.0

Function ajFeatSetScore

Prototype

void ajFeatSetScore (
      AjPFeature thys,
      float score
);

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

From EMBOSS 4.0.0

Function ajFeatSetStrand

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

From EMBOSS 4.0.0

Function ajFeatTagSetC

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 "corrected"

From EMBOSS 2.0.0

Function ajFeatTagSet

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 "corrected"

From EMBOSS 2.0.0

Function ajFeattagSpecialGff2

Prototype

AjBool ajFeattagSpecialGff2 (
      const AjPStr tag,
      AjPStr* pval
);

Type	Name	Read/Write	Description
const AjPStr	tag	Input	original tag name
AjPStr*	pval	Modify	tag value
AjBool		RETURN	ajTrue on success

From EMBOSS 6.4.0

Function ajFeattagSpecialGff3

Prototype

AjBool ajFeattagSpecialGff3 (
      const AjPStr tag,
      AjPStr* pval
);

Type	Name	Read/Write	Description
const AjPStr	tag	Input	original tag name
AjPStr*	pval	Modify	tag value
AjBool		RETURN	ajTrue on success

From EMBOSS 6.4.0

Function ajFeatTagAddCC

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"

From EMBOSS 2.4.0

Function ajFeatTagAddCS

Prototype

AjBool ajFeatTagAddCS (
      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"

From EMBOSS 2.4.0

Function ajFeatTagAddSS

Prototype

AjBool ajFeatTagAddSS (
      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"

From EMBOSS 2.0.0

Function ajFeatTagAddTag

Prototype

AjBool ajFeatTagAddTag (
      AjPFeature thys,
      const AjPTagval tagval
);

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

From EMBOSS 6.5.0

Function ajFeattagSpecial

Prototype

AjBool ajFeattagSpecial (
      const AjPStr tag,
      AjPStr* pval
);

Type	Name	Read/Write	Description
const AjPStr	tag	Input	original tag name
AjPStr*	pval	Modify	parameter value
AjBool		RETURN	ajTrue on success

From EMBOSS 6.4.0

Function ajFeattableNew

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

From EMBOSS 2.0.0

Function ajFeattableReset

Prototype

void ajFeattableReset (
      AjPFeattable thys,
      const AjPStr name
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Feature table
const AjPStr	name	Input	Name for new feature table
void		RETURN

From EMBOSS 6.6.0

Function ajFeattableSetCircular

Prototype

void ajFeattableSetCircular (
      AjPFeattable thys
);

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

From EMBOSS 6.5.0

Function ajFeattableSetDefname

Prototype

void ajFeattableSetDefname (
      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

From EMBOSS 6.2.0

Function ajFeattableSetLength

Prototype

void ajFeattableSetLength (
      AjPFeattable thys,
      ajuint len
);

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

From EMBOSS 6.0.0

Function ajFeattableSetLinear

Prototype

void ajFeattableSetLinear (
      AjPFeattable thys
);

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

From EMBOSS 6.5.0

Function ajFeattableSetNuc

Prototype

void ajFeattableSetNuc (
      AjPFeattable thys
);

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

From EMBOSS 4.0.0

Function ajFeattableSetProt

Prototype

void ajFeattableSetProt (
      AjPFeattable thys
);

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

From EMBOSS 2.1.0

Function ajFeattableSetRange

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

From EMBOSS 2.5.0

Function ajFeattableSetReverse

Prototype

void ajFeattableSetReverse (
      AjPFeattable thys
);

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

From EMBOSS 6.6.0

Function ajFeattableReverse

Prototype

void ajFeattableReverse (
      AjPFeattable thys
);

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

From EMBOSS 2.5.0

Function ajFeatReverse

Prototype

void ajFeatReverse (
      AjPFeature thys,
      ajint ilen
);

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

From EMBOSS 2.5.0

Function ajFeattableNewDna

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

From EMBOSS 2.0.0

Function ajFeattableNewSeq

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

From EMBOSS 2.0.0

Function ajFeattableNewProt

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

From EMBOSS 2.0.0

Function ajFeatGfftagAddCS

Prototype

ajuint ajFeatGfftagAddCS (
      AjPFeature thys,
      const char* tag,
      const AjPStr value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const char*	tag	Input	Tag name
const AjPStr	value	Input	Tag value list
ajuint		RETURN	Number of values added

From EMBOSS 6.4.0

Function ajFeatGfftagAddSS

Prototype

ajuint ajFeatGfftagAddSS (
      AjPFeature thys,
      const AjPStr tag,
      const AjPStr value
);

Type	Name	Read/Write	Description
AjPFeature	thys	Modify	Feature
const AjPStr	tag	Input	Tag name
const AjPStr	value	Input	Tag value list
ajuint		RETURN	Number of values added

From EMBOSS 6.4.0

Function ajFeatGfftagAddTag

Prototype

AjBool ajFeatGfftagAddTag (
      AjPFeature thys,
      const AjPTagval tagval
);

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

From EMBOSS 6.5.0

Function ajFeattableNewFtable

Prototype

AjPFeattable ajFeattableNewFtable (
      const AjPFeattable orig
);

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

From EMBOSS 6.2.0

Function ajFeattableNewFtableLimit

Prototype

AjPFeattable ajFeattableNewFtableLimit (
      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

From EMBOSS 6.2.0

Function ajFeatNewFeat

Prototype

AjPFeature ajFeatNewFeat (
      const AjPFeature orig
);

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

From EMBOSS 6.2.0

Function ajFeatTrace

Prototype

void ajFeatTrace (
      const AjPFeature thys
);

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

From EMBOSS 1.0.0

Function ajFeatTagTrace

Prototype

void ajFeatTagTrace (
      const AjPFeature thys
);

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

From EMBOSS 2.0.0

Function ajFeatGfftagTrace

Prototype

void ajFeatGfftagTrace (
      const AjPFeature thys
);

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

From EMBOSS 6.5.0

Function ajFeatGfftagsNew

Prototype

AjPFeatGfftags ajFeatGfftagsNew (
      void
);

Type	Name	Read/Write	Description
AjPFeatGfftags		RETURN	GFF tag-values structure

From EMBOSS 6.4.0

Function ajFeatGfftagsDel

Prototype

void ajFeatGfftagsDel (
      AjPFeatGfftags* Pthys
);

Type	Name	Read/Write	Description
AjPFeatGfftags*	Pthys	Delete	GFF tag-values structure
void		RETURN

From EMBOSS 6.4.0

Function ajFeatGetGfftags

Prototype

AjPFeatGfftags ajFeatGetGfftags (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
AjPFeatGfftags		RETURN	Gff tags object

From EMBOSS 6.4.0

Function ajFeatGetId

Prototype

const AjPStr ajFeatGetId (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
const AjPStr		RETURN	ID tag

From EMBOSS 6.5.0

Function ajFeatGetParent

Prototype

const AjPStr ajFeatGetParent (
      const AjPFeature thys
);

Type	Name	Read/Write	Description
const AjPFeature	thys	Input	Feature
const AjPStr		RETURN	Parent tag

From EMBOSS 6.4.0

Function ajFeatTagIter

Prototype

AjIList ajFeatTagIter (
      const AjPFeature thys
);

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

From EMBOSS 2.0.0

Function ajFeatSubIter

Prototype

AjIList ajFeatSubIter (
      const AjPFeature thys
);

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

From EMBOSS 6.4.0

Function ajFeatTagval

Prototype

AjBool ajFeatTagval (
      AjIList iter,
      AjPStr* Ptagnam,
      AjPStr* Ptagval
);

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

From EMBOSS 2.0.0

Function ajFeattableTrace

Prototype

void ajFeattableTrace (
      const AjPFeattable thys
);

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

From EMBOSS 2.0.0

Function ajFeatTypeNuc

Prototype

const AjPStr ajFeatTypeNuc (
      const AjPStr type
);

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

From EMBOSS 6.0.0

Function ajFeatTypeProt

Prototype

const AjPStr ajFeatTypeProt (
      const AjPStr type
);

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

From EMBOSS 6.0.0

Function ajFeattypeGetExternal

Prototype

const AjPStr ajFeattypeGetExternal (
      const AjPStr type,
      const AjPTable table
);

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

From EMBOSS 6.4.0

Function ajFeattypeGetInternal

Prototype

const AjPStr ajFeattypeGetInternal (
      const AjPStr type
);

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

From EMBOSS 6.4.0

Function ajFeattypeGetInternalEmbl

Prototype

const AjPStr ajFeattypeGetInternalEmbl (
      const AjPStr type
);

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

From EMBOSS 6.4.0

Function ajFeattypeGetInternalNuc

Prototype

const AjPStr ajFeattypeGetInternalNuc (
      const AjPStr type
);

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

From EMBOSS 6.4.0

Function ajFeattypeGetInternalPir

Prototype

const AjPStr ajFeattypeGetInternalPir (
      const AjPStr type
);

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

From EMBOSS 6.4.0

Function ajFeattypeGetInternalProt

Prototype

const AjPStr ajFeattypeGetInternalProt (
      const AjPStr type
);

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

From EMBOSS 6.4.0

Function ajFeattypeGetInternalRefseqp

Prototype

const AjPStr ajFeattypeGetInternalRefseqp (
      const AjPStr type
);

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

From EMBOSS 6.4.0

Function ajFeattagGetNameC

Prototype

const AjPStr ajFeattagGetNameC (
      const char* tag,
      const AjPTable table,
      AjBool* knowntag
);

Type	Name	Read/Write	Description
const char*	tag	Input	Type name
const AjPTable	table	Input	Feature table
AjBool*	knowntag	Output	ajTrue if the tag name is known ajFalse if the default name was substituted
const AjPStr		RETURN	Valid feature tag name

From EMBOSS 6.4.0

Function ajFeattagGetNameS

Prototype

const AjPStr ajFeattagGetNameS (
      const AjPStr tag,
      const AjPTable table,
      AjBool* knowntag
);

Type	Name	Read/Write	Description
const AjPStr	tag	Input	Type name
const AjPTable	table	Input	Feature table
AjBool*	knowntag	Output	ajTrue if the tag was found in the list of known tags
const AjPStr		RETURN	Valid feature tag name

From EMBOSS 6.4.0

Function ajFeattagFormat

Prototype

void ajFeattagFormat (
      const AjPStr name,
      const AjPTable table,
      AjPStr* retstr
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	Tag name
const AjPTable	table	Input	Tag table
AjPStr*	retstr	Output	string with formatted value.
void		RETURN

From EMBOSS 6.4.0

Function ajFeattagGetLimit

Prototype

void ajFeattagGetLimit (
      const AjPStr name,
      const AjPTable table,
      AjPStr* retstr
);

Type	Name	Read/Write	Description
const AjPStr	name	Input	Tag name
const AjPTable	table	Input	Tag table
AjPStr*	retstr	Output	string with formatted value.
void		RETURN

From EMBOSS 6.4.0

Function ajFeatUnused

Prototype

void ajFeatUnused (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 1.0.0

Function ajFeatTypeIsCds

Prototype

AjBool ajFeatTypeIsCds (
      const AjPFeature gf
);

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

From EMBOSS 6.0.0

Function ajFeatTypeMatchC

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

From EMBOSS 6.1.0

Function ajFeatTypeMatchS

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

From EMBOSS 6.1.0

Function ajFeatTypeMatchWildS

Prototype

AjBool ajFeatTypeMatchWildS (
      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

From EMBOSS 6.2.0

Function ajFeatIsLocal

Prototype

AjBool ajFeatIsLocal (
      const AjPFeature gf
);

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

From EMBOSS 2.1.0

Function ajFeatIsLocalRange

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

From EMBOSS 2.1.0

Function ajFeatIsMultiple

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

From EMBOSS 2.5.0

Function ajFeatIsCompMult

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

From EMBOSS 2.5.0

Function ajFeattablePos

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.

From EMBOSS 2.5.0

Function ajFeattablePosI

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.

From EMBOSS 2.5.0

Function ajFeattablePosII

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.

From EMBOSS 2.5.0

Function ajFeattableTrimOff

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.

From EMBOSS 2.7.0

Function ajFeattableTrim

Prototype

AjBool ajFeattableTrim (
      AjPFeattable thys
);

Type	Name	Read/Write	Description
AjPFeattable	thys	Modify	Target feature table.
AjBool		RETURN	AjTrue returned if successful.

From EMBOSS 6.3.0

Function ajFeatTrimOffRange

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. ajFalse returned if feature could not be trimmed

From EMBOSS 2.7.0

Function ajFeattagIsNote

Prototype

AjBool ajFeattagIsNote (
      const AjPStr tag
);

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

From EMBOSS 6.0.0

Function ajFeatExit

Prototype

void ajFeatExit (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 2.0.0

Function ajFeatWarn

Prototype

void ajFeatWarn (
      const char* fmt,
      ...
);

Type	Name	Read/Write	Description
const char*	fmt	Input	Format string
...	vararg	Vararg	Format arguments.
void		RETURN

From EMBOSS 6.4.0