ajfeat.c

Section: Feature Object Constructors

All constructors return a new feature or feature table set by pointer. It is the responsibility of the user to first destroy any previous feature. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

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!

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

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

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 ajFeatNewSub

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

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

Simple constructor with only start and end positions

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

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

Simple constructor with only start and end positions

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

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

Simple constructor with only start and end positions, sets feature to be on the reverse strand

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

Simple constructor with only start and end positions, sets feature to be on the reverse strand

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

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

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

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

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

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

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

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

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

Compare two features by their start.

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.

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

Compare two features by their end.

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.

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

Compare two features by their group and exon numbers

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.

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

Compare two features by their type (key).

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.

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

Constructor for a new feature, automatically added to the specified table.

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

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

Constructor for a new feature, automatically added to the specified table.

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

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

Constructor for a new feature, automatically added to the specified table.

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

Constructor for a new feature, automatically added to the specified table.

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

(Simple minded) object destruction by release of memory.

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

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

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

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

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

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

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

Sort Feature table by Type.

Prototype

void ajFeatSortByType (
      AjPFeattable Feattab
);

Type Name Read/Write Description

AjPFeattable Feattab Modify Feature table to be sorted.

void RETURN

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

From EMBOSS 1.0.0

Function ajFeatSortByStart

Sort Feature table by Start position.

Prototype

void ajFeatSortByStart (
      AjPFeattable Feattab
);

Type Name Read/Write Description

AjPFeattable Feattab Modify Feature table to be sorted.

void RETURN

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

From EMBOSS 1.0.0

Function ajFeatSortByEnd

Sort Feature table by End position.

Prototype

void ajFeatSortByEnd (
      AjPFeattable Feattab
);

Type Name Read/Write Description

AjPFeattable Feattab Modify Feature table to be sorted.

void RETURN

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

Function ajFeattableAdd

Method to add a new AjPFeature to a AjPFeattable

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

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

Section: Feature Object Operators

These functions use the contents of a feature object, but do not make any changes.

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.

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.

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

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.

ajFeatTagAddC Sets a feature tag value, creating a new feature tag even if one already exists.

ajFeatTagAdd 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.

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.

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

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

ajFeatGfftagAddC Constructor for a feature GFF3 tag-value pair

ajFeatGfftagAdd Constructor for a feature GFF3 tag-value pair

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

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

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.)

ajFeatIsChild Tests whether the feature is a child member of a join The parent (first) feature of a join gives: ajFeatIsChild == ajFalse && ajFeatIsMultiple == ajTrue

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

Clears a feature table of all features

Prototype

void ajFeattableClear (
      AjPFeattable thys
);

Type Name Read/Write Description

AjPFeattable thys Modify Feature table

void RETURN

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

From EMBOSS 2.1.0

Function ajFeatTypeGetCategory

returns the category name for a feature type

Prototype

const AjPStr ajFeatTypeGetCategory (
      const AjPStr type
);

Type Name Read/Write Description

const AjPStr type Input Feature type

const AjPStr RETURN Feature category

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

From EMBOSS 6.1.0

Function ajFeattableGetEntry

Return the full text

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

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

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.

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.

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.

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

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.

Prototype

const char* ajFeattableGetTypeC (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

const char* RETURN Feature table type.

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

From EMBOSS 4.0.0

Function 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.

Prototype

const AjPStr ajFeattableGetTypeS (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

const AjPStr RETURN Feature table name.

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

From EMBOSS 4.0.0

Function ajFeattableGetXrefs

Returns all cross-references from a feature table

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

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

Converts a frame number in the range 0 to 3 to a GFF frame character or '.' as the general default

Prototype

char ajFeatframeGetFrame (
      ajint frame
);

Type Name Read/Write Description

ajint frame Input Feature frame number

char RETURN character for this frame in GFF

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

Converts a frame number in the range 0 to 3 to a GFF frame character or '0' for the nucleotide default

Prototype

char ajFeatframeGetFrameNuc (
      ajint frame
);

Type Name Read/Write Description

ajint frame Input Feature frame number

char RETURN character for this frame in GFF

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

Converts a strand number to a GFF strand character. NULL characters are converted to '+' All other values are simply cast to character.

Prototype

char ajFeatstrandGetStrand (
      ajint strand
);

Type Name Read/Write Description

ajint strand Input Strand

char RETURN GFF character for this strand.

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

From EMBOSS 6.4.0

Function ajFeattableIsNuc

Returns ajTrue if a feature table is nucleotide

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

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

Returns ajTrue if a feature table is protein

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

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

Returns the feature table start position, or 1 if no start has been set.

Prototype

ajint ajFeattableGetBegin (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input feature table object

ajint RETURN Start position.

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

From EMBOSS 6.2.0

Function ajFeattableGetEnd

Returns the features table end position, or the feature table length if no end has been set.

Prototype

ajint ajFeattableGetEnd (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input feature table object

ajint RETURN End position.

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

From EMBOSS 6.2.0

Function ajFeattableGetLen

Returns the sequence length of a feature table

Prototype

ajint ajFeattableGetLen (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

ajint RETURN Length in bases or residues

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

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.

Prototype

const AjPStr ajFeattableGetName (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

const AjPStr RETURN Feature table name.

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

From EMBOSS 2.1.0

Function ajFeattableGetSize

Returns the size of a feature table object.

Prototype

ajuint ajFeattableGetSize (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

ajuint RETURN Feature table size.

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

From EMBOSS 6.1.0

Function 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.

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

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

Returns the sequence matching a feature.

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

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

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.

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

Returns a sequence entry from a feature location which points to another entry

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 ajFeatGetXrefs

Returns all cross-references from a feature

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

Returns a sequence entry converted to lower case where a feature location matches.

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

Finds a named note tag (with a * prefix)

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

Finds a named note tag (with a * prefix)

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

Finds a named note tag (with a * prefix)

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

Finds a named note tag (with a * prefix)

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

Returns the nth value of a named feature tag.

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

Returns the nth value of a named feature tag.

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

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.

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

Returns the source name of a feature object.

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

Returns the start position of a feature object.

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

Returns the strand of a feature object.

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

Returns the end position of a feature object.

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

Returns the sequence length of a feature object.

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

Returns the score of a feature object.

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

Returns the direction of a feature object.

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

Returns the reading frame of a feature object.

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

Returns translation tag value

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

Temporary testing function for feature handling to be deleted when all is working happily

Prototype

void ajFeatTest (
      void
);

Type Name Read/Write Description

void RETURN

From EMBOSS 2.0.0

Function ajFeatVocabGetTags

Returns tags table for a named feature format

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

Returns tags table for a named nucleotide feature format

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

Returns tags table for a named protein feature format

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

Returns types table for a named feature format

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

Returns types table for a named nucleotide feature format

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

Returns types table for a named protein feature format

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

Initialises feature table internals for a named feature format

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

Initialises feature table internals for a named feature format

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

Initialises feature table internals for a named feature format

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

Sets the description for a feature

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

Sets the description for a feature

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

Sets the source for a feature

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

Sets the score for a feature

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

Sets the strand for a feature

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

Sets a feature tag value

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

Sets a feature tag value

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

Special processing for known GFF tags

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

Special processing for known GFF3 tags

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

Sets a feature tag value, creating a new feature tag even if one already exists.

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 ajFeatTagAddC

Sets a feature tag value, creating a new feature tag even if one already exists.

Prototype

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

From EMBOSS 2.4.0

Function ajFeatTagAdd

Sets a feature tag value, creating a new feature tag even if one already exists.

Prototype

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

From EMBOSS 2.0.0

Function ajFeattagSpecial

Special processing for known internal (EMBL) tags

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

Constructor for a new (generic) feature table. Does not define the feature table type.

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 ajFeattableSetDefname

Provides a unique (for this program run) name for a feature table.

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

Sets the length of a feature table with the length of the source sequence.

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 ajFeattableSetNuc

Sets the type of a feature table as nucleotide

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

Sets the type of a feature table as Protein

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

Set the begin and end range for a feature table

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 ajFeattableReverse

Reverse the features in a feature table by iterating through and reversing all positions and strands.

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

Reverse one feature by reversing all positions and strand.

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

Constructor for a new DNA feature table

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

Constructor for a new feature table for an existing sequence. The feature table type is determined by the sequence type.

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

Constructor for a new protein feature table

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 ajFeatGfftagAddC

Constructor for a feature GFF3 tag-value pair

Prototype

ajuint ajFeatGfftagAddC (
      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 ajFeatGfftagAdd

Constructor for a feature GFF3 tag-value pair

Prototype

ajuint ajFeatGfftagAdd (
      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 ajFeattableNewFtable

Makes a copy of a feature table.

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

Makes a copy of a feature table using only a limited number of features.

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

Makes a copy of a feature.

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

Traces (to the debug file) a feature object

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

Traces (to the debug file) the tag-value pairs of a feature object

Prototype

void ajFeatTagTrace (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature

void RETURN

From EMBOSS 2.0.0

Function ajFeatGfftagsNew

Creates a structure holding GFF tag value pairs

Prototype

AjPFeatGfftags ajFeatGfftagsNew (
      void
);

Type Name Read/Write Description

AjPFeatGfftags RETURN GFF tag-values structure

From EMBOSS 6.4.0

Function ajFeatGfftagsDel

Destroys a structure holding GFF tag value pairs

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

Returns an object with all feature GFF tag-value pairs

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 ajFeatGetParent

Returns the GFF Parent tag of a feature with GFF tag-value pairs

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

Returns an iterator over all feature tag-value pairs

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

Returns an iterator over all subfeaturers

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

Returns the tag-value pairs of a feature object

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

Traces (to the debug file) a complete feature table

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

Given a feature type name, returns the valid feature type for the internal DNA feature table

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

Given a feature type name, returns the valid feature type for the internal protein feature table

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

Given a feature type name, returns the valid feature type for a feature table

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

Given a feature type name, returns the valid feature type for an internal feature table

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

Given a feature type name, returns the valid feature type for an EMBL format feature table

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

Given a feature type name, returns the valid feature type for an internal feature table

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

Given a feature type name, returns the valid feature type for an internal feature table

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

Given a feature type name, returns the valid feature type for an internal feature table

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

Given a feature type name, returns the valid feature type for a REFSEQP format feature table

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

Given a feature tag name, returns the valid feature tag name for a feature table

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

Given a feature tag name, returns the valid feature tag name for a feature table

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

Converts a feature tag value into the correct format, after checking it is an acceptable value

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

Returns the controlled vocabulary list for a limited value.

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

Dummy function to prevent compiler warnings

Prototype

void ajFeatUnused (
      void
);

Type Name Read/Write Description

void RETURN

From EMBOSS 1.0.0

Function ajFeatTypeIsCds

Tests whether the feature is a CDS feature

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

Tests whether the feature type matches a given string including testing for alternative names

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

Tests whether the feature type matches a given string including testing for alternative names

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

Tests whether the feature type matches a given wildcard string including testing for alternative names

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

Tests whether the feature is local to the sequence. Returns AJTRUE if it is local, AJFALSE if remote.

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

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.)

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 ajFeatIsChild

Tests whether the feature is a child member of a join The parent (first) feature of a join gives: ajFeatIsChild == ajFalse && ajFeatIsMultiple == ajTrue

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

From EMBOSS 2.5.0

Function ajFeatIsMultiple

Tests whether the feature is a member of a join, group order or one_of

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

Tests whether the feature is a member of a complement around a multiple (join, etc.)

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

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.

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

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.

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

Converts a position into a true position. If ipos is negative, it is counted from the end of the sequence rather than the beginning.

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

Trim a feature table using the Begin and Ends.

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

Trim a feature table using the Begin and Ends.

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

Trim a feature table using the Begin and Ends.

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.

From EMBOSS 2.7.0

Function ajFeattagIsNote

Tests whether the feature tag is a note (the default feature tag)

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

Cleans up feature table internal memory

Prototype

void ajFeatExit (
      void
);

Type Name Read/Write Description

void RETURN

From EMBOSS 2.0.0

Function ajFeatWarn

Formatted write as a warning message.

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

ajFeatNew	Constructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
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.

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.

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

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.
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.
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
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.
ajFeatTagAddC	Sets a feature tag value, creating a new feature tag even if one already exists.
ajFeatTagAdd	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.
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.
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
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
ajFeatGfftagAddC	Constructor for a feature GFF3 tag-value pair
ajFeatGfftagAdd	Constructor for a feature GFF3 tag-value pair
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
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
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.)
ajFeatIsChild	Tests whether the feature is a child member of a join The parent (first) feature of a join gives: ajFeatIsChild == ajFalse && ajFeatIsMultiple == ajTrue
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.

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

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

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

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

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

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

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.

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.

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