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

Function ajFeattabOutOpen

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

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

Synopsis

Prototype

AjBool ajFeattabOutOpen (
      AjPFeattabOut thys,
      const AjPStr ufo
);

Type Name Read/Write Description

AjPFeattabOut thys Modify Features table output object

const AjPStr ufo Input UFO feature output specifier

AjBool RETURN ajTrue on success

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

Input

ufo:

(Input)

UFO feature output specifier

Input & Output

thys:

(Modify)

Features table output object

Returns

AjBool:

ajTrue on success

Description

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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutFile

Returns the name of a feature output file

Synopsis

Prototype

AjPFile ajFeattabOutFile (
      const AjPFeattabOut thys
);

Type Name Read/Write Description

const AjPFeattabOut thys Input Features table output object

AjPFile RETURN File object

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

Input

thys:

(Input)

Features table output object

Returns

AjPFile:

File object

Description

Returns the name of a feature output file

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutFilename

Returns the name of a feature output file

Synopsis

Prototype

AjPStr ajFeattabOutFilename (
      const AjPFeattabOut thys
);

Type Name Read/Write Description

const AjPFeattabOut thys Input Features table output object

AjPStr RETURN Filename

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

Input

thys:

(Input)

Features table output object

Returns

AjPStr:

Filename

Description

Returns the name of a feature output file

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutIsOpen

Checks whether feature output file has already been opened

Synopsis

Prototype

AjBool ajFeattabOutIsOpen (
      const AjPFeattabOut thys
);

Type Name Read/Write Description

const AjPFeattabOut thys Input Features table output object

AjBool RETURN ajTrue if file is open

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

Input

thys:

(Input)

Features table output object

Returns

AjBool:

ajTrue if file is open

Description

Checks whether feature output file has already been opened

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutIsLocal

Checks whether feature output file has already been opened

Synopsis

Prototype

AjBool ajFeattabOutIsLocal (
      const AjPFeattabOut thys
);

Type Name Read/Write Description

const AjPFeattabOut thys Input Features table output object

AjBool RETURN ajTrue if file is open

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

Input

thys:

(Input)

Features table output object

Returns

AjBool:

ajTrue if file is open

Description

Checks whether feature output file has already been opened

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutSet

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

Synopsis

Prototype

AjBool ajFeattabOutSet (
      AjPFeattabOut thys,
      const AjPStr ufo
);

Type Name Read/Write Description

AjPFeattabOut thys Modify Features table output object

const AjPStr ufo Input UFO feature output specifier

AjBool RETURN ajTrue on success

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

Input

ufo:

(Input)

UFO feature output specifier

Input & Output

thys:

(Modify)

Features table output object

Returns

AjBool:

ajTrue on success

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInNew

Constructor for an empty feature table input object

Synopsis

Prototype

AjPFeattabIn ajFeattabInNew (
      void
);

Type Name Read/Write Description

AjPFeattabIn RETURN Feature table input object

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

Returns

AjPFeattabIn:

Feature table input object

Description

Constructor for an empty feature table input object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInNewSS

Constructor for an empty feature table input object. The format and name are read.

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPStr fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFeattabIn RETURN Feature table input object

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Returns

AjPFeattabIn:

Feature table input object

Description

Constructor for an empty feature table input object. The format and name are read.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInNewCSF

Constructor for an empty feature table input object. The format and name are read. The file buffer is moved to the feature table input object and should not be deleted by the calling program.

Synopsis

Prototype

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

Type Name Read/Write Description

const char* fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFileBuff buff Modify Buffer containing feature data

AjPFeattabIn RETURN Feature table input object

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Input & Output

buff:

(Modify)

Buffer containing feature data

Returns

AjPFeattabIn:

Feature table input object

Description

Constructor for an empty feature table input object. The format and name are read. The file buffer is moved to the feature table input object and should not be deleted by the calling program.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInNewSSF

Constructor for an empty feature table input object. The format and name are read. The file buffer is moved to the feature table input object and should not be deleted by the calling program.

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPStr fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFileBuff buff Modify Buffer containing feature data

AjPFeattabIn RETURN Feature table input object

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Input & Output

buff:

(Modify)

Buffer containing feature data

Returns

AjPFeattabIn:

Feature table input object

Description

Constructor for an empty feature table input object. The format and name are read. The file buffer is moved to the feature table input object and should not be deleted by the calling program.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutNew

Constructor for an empty feature table output object

Synopsis

Prototype

AjPFeattabOut ajFeattabOutNew (
      void
);

Type Name Read/Write Description

AjPFeattabOut RETURN Feature table input object

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

Returns

AjPFeattabOut:

Feature table input object

Description

Constructor for an empty feature table output object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutSetBasename

Sets the base output filename for feature table output

Synopsis

Prototype

void ajFeattabOutSetBasename (
      AjPFeattabOut thys,
      const AjPStr basename
);

Type Name Read/Write Description

AjPFeattabOut thys Modify feature table output

const AjPStr basename Input Output base filename

void RETURN

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

Input

basename:

(Input)

Output base filename

Input & Output

thys:

(Modify)

feature table output

Returns

void:

No return value

Description

Sets the base output filename for feature table output

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutNewCSF

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

Synopsis

Prototype

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

Type Name Read/Write Description

const char* fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFile file Modify Output file

AjPFeattabOut RETURN Feature table output object

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Input & Output

file:

(Modify)

Output file

Returns

AjPFeattabOut:

Feature table output object

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutNewSSF

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

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPStr fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFile file Modify Output file

AjPFeattabOut RETURN Feature table output object

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Input & Output

file:

(Modify)

Output file

Returns

AjPFeattabOut:

Feature table output object

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatRead

Generic interface function for reading in features from a file given the file handle, class of map, data format of input and possibly other associated data.

Synopsis

Prototype

AjPFeattable ajFeatRead (
      AjPFeattabIn ftin
);

Type Name Read/Write Description

AjPFeattabIn ftin Modify Specifies the external source (file) of the features to be read in

AjPFeattable RETURN Pointer to a new feature table containing the features read in

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

Input & Output

ftin:

(Modify)

Specifies the external source (file) of the features to be read in

Returns

AjPFeattable:

Pointer to a new feature table containing the features read in

Description

Generic interface function for reading in features from a file given the file handle, class of map, data format of input and possibly other associated data.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatNew

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

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeattable thys Modify Pointer to the ajFeattable which will own the feature

const AjPStr source Input Analysis basis for feature

const AjPStr type Input Type of feature (e.g. exon)

ajint Start Input Start position of the feature

ajint End Input End position of the feature

float score Input Analysis score for the feature

char strand Input Strand of the feature

ajint frame Input Frame of the feature

AjPFeature RETURN newly allocated feature object

Input

source:	(Input)	Analysis basis for feature
type:	(Input)	Type of feature (e.g. exon)
Start:	(Input)	Start position of the feature
End:	(Input)	End position of the feature
score:	(Input)	Analysis score for the feature
strand:	(Input)	Strand of the feature
frame:	(Input)	Frame of the feature

Input & Output

thys:

(Modify)

Pointer to the ajFeattable which will own the feature

Returns

AjPFeature:

newly allocated feature object

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatNewII

Simple constructor with only start and end positions

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

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeattable thys Modify Pointer to the ajFeattable which will own the feature

ajint Start Input Start position of the feature

ajint End Input End position of the feature

AjPFeature RETURN newly allocated feature object

Input

Start:	(Input)	Start position of the feature
End:	(Input)	End position of the feature

Input & Output

thys:

(Modify)

Pointer to the ajFeattable which will own the feature

Returns

AjPFeature:

newly allocated feature object

Description

Simple constructor with only start and end positions

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatNewIIRev

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

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

Synopsis

Prototype

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

Input

Start:	(Input)	Start position of the feature
End:	(Input)	End position of the feature

Input & Output

thys:

(Modify)

Pointer to the ajFeattable which will own the feature

Returns

AjPFeature:

newly allocated feature object

Description

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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatNewProt

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

Synopsis

Prototype

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

Input

source:	(Input)	Analysis basis for feature
type:	(Input)	Type of feature (e.g. exon)
Start:	(Input)	Start position of the feature
End:	(Input)	End position of the feature
score:	(Input)	Analysis score for the feature

Input & Output

thys:

(Modify)

Pointer to the ajFeattable which will own the feature

Returns

AjPFeature:

newly allocated feature object

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Section: Feature Object Destructors

(Simple minded) object destruction by release of memory.

No reference counting (for now).

Functions: ajFeattabInDel ajFeattableDel ajFeatDel

Function ajFeattabInDel

Destructor for a feature table input object

Synopsis

Prototype

void ajFeattabInDel (
      AjPFeattabIn* pthis
);

Type Name Read/Write Description

AjPFeattabIn* pthis Delete Feature table input object

void RETURN

Output

pthis:

(Delete)

Feature table input object

Returns

void:

No return value

Description

Destructor for a feature table input object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableDel

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

Synopsis

Prototype

void ajFeattableDel (
      AjPFeattable* pthis
);

Type Name Read/Write Description

AjPFeattable* pthis Delete Pointer to the object to be deleted. The pointer is always deleted.

void RETURN

Output

pthis:

(Delete)

Pointer to the object to be deleted. The pointer is always deleted.

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatDel

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

Synopsis

Prototype

void ajFeatDel (
      AjPFeature* pthis
);

Type Name Read/Write Description

AjPFeature* pthis Delete Pointer to the object to be deleted. The pointer is always deleted.

void RETURN

Output

pthis:

(Delete)

Pointer to the object to be deleted. The pointer is always deleted.

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Section: Feature Assignments

Functions: ajFeatUfoWrite ajFeattableWrite ajFeatSortByType ajFeatSortByStart ajFeatSortByEnd

Function ajFeatUfoWrite

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

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPFeattable thys Input Feature table to be written

AjPFeattabOut featout Modify Feature output object

const AjPStr ufo Input UFO feature spec (ignored if already open)

AjBool RETURN ajTrue on success.

Input

thys:	(Input)	Feature table to be written
ufo:	(Input)	UFO feature spec (ignored if already open)

Input & Output

featout:

(Modify)

Feature output object

Returns

AjBool:

ajTrue on success.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWrite

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

Synopsis

Prototype

AjBool ajFeattableWrite (
      AjPFeattable thys,
      const AjPStr ufo
);

Type Name Read/Write Description

AjPFeattable thys Output Feature table created

const AjPStr ufo Input UFO feature spec

AjBool RETURN ajTrue on success.

Input

ufo:

(Input)

UFO feature spec

Output

thys:

(Output)

Feature table created

Returns

AjBool:

ajTrue on success.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSortByType

Sort Feature table by Type.

Synopsis

Prototype

void ajFeatSortByType (
      AjPFeattable Feattab
);

Type Name Read/Write Description

AjPFeattable Feattab Modify Feature table to be sorted.

void RETURN

Input & Output

Feattab:

(Modify)

Feature table to be sorted.

Returns

void:

No return value

Description

Sort Feature table by Type.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSortByStart

Sort Feature table by Start position.

Synopsis

Prototype

void ajFeatSortByStart (
      AjPFeattable Feattab
);

Type Name Read/Write Description

AjPFeattable Feattab Modify Feature table to be sorted.

void RETURN

Input & Output

Feattab:

(Modify)

Feature table to be sorted.

Returns

void:

No return value

Description

Sort Feature table by Start position.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSortByEnd

Sort Feature table by End position.

Synopsis

Prototype

void ajFeatSortByEnd (
      AjPFeattable Feattab
);

Type Name Read/Write Description

AjPFeattable Feattab Modify Feature table to be sorted.

void RETURN

Input & Output

Feattab:

(Modify)

Feature table to be sorted.

Returns

void:

No return value

Description

Sort Feature table by End position.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Section: Feature Table Modifiers

Functions: ajFeattableAdd

Function ajFeattableAdd

Method to add a new AjPFeature to a AjPFeattable

Synopsis

Prototype

void ajFeattableAdd (
      AjPFeattable thys,
      AjPFeature feature
);

Type Name Read/Write Description

AjPFeattable thys Modify The feature table

AjPFeature feature Modify Feature to be added to the set

void RETURN

Input & Output

thys:	(Modify)	The feature table
feature:	(Modify)	Feature to be added to the set

Returns

void:

No return value

Description

Method to add a new AjPFeature to a AjPFeattable

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Section: Feature Object Operators

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

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

Function ajFeattableClear

Clears a feature table of all features

Synopsis

Prototype

void ajFeattableClear (
      AjPFeattable thys
);

Type Name Read/Write Description

AjPFeattable thys Modify Feature table

void RETURN

Input & Output

thys:

(Modify)

Feature table

Returns

void:

No return value

Description

Clears a feature table of all features

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatOutFormatDefault

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

Synopsis

Prototype

AjBool ajFeatOutFormatDefault (
      AjPStr* pformat
);

Type Name Read/Write Description

AjPStr* pformat Output Default output feature format.

AjBool RETURN ajTrue on success.

Output

pformat:

(Output)

Default output feature format.

Returns

AjBool:

ajTrue on success.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatWrite

Generic interface function for writing features from a file given the file handle, class of map, data format of input and possibly other associated data.

Synopsis

Prototype

AjBool ajFeatWrite (
      AjPFeattabOut ftout,
      const AjPFeattable features
);

Type Name Read/Write Description

AjPFeattabOut ftout Modify Specifies the external source (file) of the features to be written

const AjPFeattable features Input Feature set to be written out

AjBool RETURN Returns ajTrue if successful; ajFalse otherwise

Input

features:

(Input)

Feature set to be written out

Input & Output

ftout:

(Modify)

Specifies the external source (file) of the features to be written

Returns

AjBool:

Returns ajTrue if successful; ajFalse otherwise

Description

Generic interface function for writing features from a file given the file handle, class of map, data format of input and possibly other associated data.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWriteGff2

Write feature table in GFF 2.0 format

Synopsis

Prototype

AjBool ajFeattableWriteGff2 (
      const AjPFeattable Feattab,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable Feattab Input feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

Feattab:

(Input)

feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write feature table in GFF 2.0 format

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWriteGff3

Write feature table in GFF format

Synopsis

Prototype

AjBool ajFeattableWriteGff3 (
      const AjPFeattable Feattab,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable Feattab Input feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

Feattab:

(Input)

feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write feature table in GFF format

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWriteDdbj

Write a feature table in DDBJ format.

Synopsis

Prototype

AjBool ajFeattableWriteDdbj (
      const AjPFeattable thys,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

thys:

(Input)

Feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write a feature table in DDBJ format.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWriteEmbl

Write a feature table in EMBL format.

Synopsis

Prototype

AjBool ajFeattableWriteEmbl (
      const AjPFeattable thys,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

thys:

(Input)

Feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write a feature table in EMBL format.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWriteGenbank

Write a feature table in GenBank format.

Synopsis

Prototype

AjBool ajFeattableWriteGenbank (
      const AjPFeattable thys,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

thys:

(Input)

Feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write a feature table in GenBank format.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWriteSwiss

Write a feature table in SwissProt format.

Synopsis

Prototype

AjBool ajFeattableWriteSwiss (
      const AjPFeattable thys,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

thys:

(Input)

Feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write a feature table in SwissProt format.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableWritePir

Write a feature table in PIR format.

Synopsis

Prototype

AjBool ajFeattableWritePir (
      const AjPFeattable thys,
      AjPFile file
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjPFile file Modify Output file

AjBool RETURN ajTrue on success

Input

thys:

(Input)

Feature table

Input & Output

file:

(Modify)

Output file

Returns

AjBool:

ajTrue on success

Description

Write a feature table in PIR format.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

Synopsis

Prototype

const AjPStr ajFeattableGetName (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

const AjPStr RETURN Feature table name.

Input

thys:

(Input)

Feature table

Returns

const AjPStr:

Feature table name.

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

Synopsis

Prototype

const char* ajFeattableGetTypeC (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

const char* RETURN Feature table type.

Input

thys:

(Input)

Feature table

Returns

const char*:

Feature table type.

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

Synopsis

Prototype

const AjPStr ajFeattableGetTypeS (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

const AjPStr RETURN Feature table name.

Input

thys:

(Input)

Feature table

Returns

const AjPStr:

Feature table name.

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableIsNuc

Returns ajTrue if a feature table is knucleotide protein

Synopsis

Prototype

AjBool ajFeattableIsNuc (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjBool RETURN ajTrue for a protein feature table

Input

thys:

(Input)

Feature table

Returns

AjBool:

ajTrue for a protein feature table

Description

Returns ajTrue if a feature table is knucleotide protein

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableIsProt

Returns ajTrue if a feature table is protein

Synopsis

Prototype

AjBool ajFeattableIsProt (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

AjBool RETURN ajTrue for a protein feature table

Input

thys:

(Input)

Feature table

Returns

AjBool:

ajTrue for a protein feature table

Description

Returns ajTrue if a feature table is protein

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableBegin

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

Synopsis

Prototype

ajint ajFeattableBegin (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input feature table object

ajint RETURN Start position.

Input

thys:

(Input)

feature table object

Returns

ajint:

Start position.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableEnd

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

Synopsis

Prototype

ajint ajFeattableEnd (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input feature table object

ajint RETURN End position.

Input

thys:

(Input)

feature table object

Returns

ajint:

End position.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableLen

Returns the sequence length of a feature table

Synopsis

Prototype

ajint ajFeattableLen (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

ajint RETURN Length in bases or residues

Input

thys:

(Input)

Feature table

Returns

ajint:

Length in bases or residues

Description

Returns the sequence length of a feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableSize

Returns the number of features in a feature table

Synopsis

Prototype

ajint ajFeattableSize (
      const AjPFeattable thys
);

Type Name Read/Write Description

const AjPFeattable thys Input Feature table

ajint RETURN Number of features

Input

thys:

(Input)

Feature table

Returns

ajint:

Number of features

Description

Returns the number of features in a feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInClear

Clears a Tabin input object back to "as new" condition, except for the USA list which must be preserved.

Synopsis

Prototype

void ajFeattabInClear (
      AjPFeattabIn thys
);

Type Name Read/Write Description

AjPFeattabIn thys Modify Sequence input

void RETURN

Input & Output

thys:

(Modify)

Sequence input

Returns

void:

No return value

Description

Clears a Tabin input object back to "as new" condition, except for the USA list which must be preserved.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatLocToSeq

Returns a sequence entry from a feature location

Synopsis

Prototype

AjBool ajFeatLocToSeq (
      const AjPStr seq,
      const AjPStr line,
      AjPStr* res,
      const AjPStr usa
);

Type Name Read/Write Description

const AjPStr seq Input sequence

const AjPStr line Input location

AjPStr* res Output sequence construct

const AjPStr usa Input usa of query

AjBool RETURN true on success

Input

seq:	(Input)	sequence
line:	(Input)	location
usa:	(Input)	usa of query

Output

res:

(Output)

sequence construct

Returns

AjBool:

true on success

Description

Returns a sequence entry from a feature location

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatLocMark

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

Synopsis

Prototype

AjBool ajFeatLocMark (
      AjPStr* seq,
      const AjPStr line
);

Type Name Read/Write Description

AjPStr* seq Modify Upper case sequence

const AjPStr line Input location

AjBool RETURN true on success

Input

line:

(Input)

location

Input & Output

seq:

(Modify)

Upper case sequence

Returns

AjBool:

true on success

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetLocs

Returns location information from catenated sequence entry

Synopsis

Prototype

ajuint ajFeatGetLocs (
      const AjPStr str,
      AjPStr** cds,
      const char* type
);

Type Name Read/Write Description

const AjPStr str Input catenated (seq->TextPtr) entry

AjPStr** cds Output array of locations

const char* type Input type (e.g. CDS/mrna)

ajuint RETURN number of location lines

Input

str:	(Input)	catenated (seq->TextPtr) entry
type:	(Input)	type (e.g. CDS/mrna)

Output

cds:

(Output)

array of locations

Returns

ajuint:

number of location lines

Description

Returns location information from catenated sequence entry

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetNote

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const AjPStr name Input Tag name

AjPStr* val Output Tag value (if found)

AjBool RETURN ajTrue on success (feature tag found)

Input

thys:	(Input)	Feature object
name:	(Input)	Tag name

Output

val:

(Output)

Tag value (if found)

Returns

AjBool:

ajTrue on success (feature tag found)

Description

Finds a named note tag (with a * prefix)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetNoteC

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const char* name Input Tag name

AjPStr* val Output Tag value (if found)

AjBool RETURN ajTrue on success (feature tag found)

Input

thys:	(Input)	Feature object
name:	(Input)	Tag name

Output

val:

(Output)

Tag value (if found)

Returns

AjBool:

ajTrue on success (feature tag found)

Description

Finds a named note tag (with a * prefix)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetNoteCI

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const char* name Input Tag name

ajint count Input Tag count: zero for any, 1 for first, 2 for second

AjPStr* val Output Tag value (if found)

AjBool RETURN ajTrue on success (feature tag found)

Input

thys:	(Input)	Feature object
name:	(Input)	Tag name
count:	(Input)	Tag count: zero for any, 1 for first, 2 for second

Output

val:

(Output)

Tag value (if found)

Returns

AjBool:

ajTrue on success (feature tag found)

Description

Finds a named note tag (with a * prefix)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetNoteI

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const AjPStr name Input Tag name

ajint count Input Tag count: zero for any, 1 for first, 2 for second

AjPStr* val Output Tag value (if found)

AjBool RETURN ajTrue on success (feature tag found)

Input

thys:	(Input)	Feature object
name:	(Input)	Tag name
count:	(Input)	Tag count: zero for any, 1 for first, 2 for second

Output

val:

(Output)

Tag value (if found)

Returns

AjBool:

ajTrue on success (feature tag found)

Description

Finds a named note tag (with a * prefix)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetTag

Returns the nth value of a named feature tag.

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

Synopsis

Prototype

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

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const AjPStr name Input Tag name

ajint num Input Tag number

AjPStr* val Output Tag value (if found)

AjBool RETURN ajTrue on success (feature tag found)

Input

thys:	(Input)	Feature object
name:	(Input)	Tag name
num:	(Input)	Tag number

Output

val:

(Output)

Tag value (if found)

Returns

AjBool:

ajTrue on success (feature tag found)

Description

Returns the nth value of a named feature tag.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

Synopsis

Prototype

const AjPStr ajFeatGetType (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const AjPStr RETURN Feature type, read only

Input

thys:

(Input)

Feature object

Returns

const AjPStr:

Feature type, read only

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetSource

Returns the source name of a feature object.

Synopsis

Prototype

const AjPStr ajFeatGetSource (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

const AjPStr RETURN Feature source name

Input

thys:

(Input)

Feature object

Returns

const AjPStr:

Feature source name

Description

Returns the source name of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetStart

Returns the start position of a feature object.

Synopsis

Prototype

ajuint ajFeatGetStart (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

ajuint RETURN Feature start position

Input

thys:

(Input)

Feature object

Returns

ajuint:

Feature start position

Description

Returns the start position of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetStrand

Returns the strand of a feature object.

Synopsis

Prototype

char ajFeatGetStrand (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

char RETURN Feature strand code

Input

thys:

(Input)

Feature object

Returns

char:

Feature strand code

Description

Returns the strand of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetEnd

Returns the end position of a feature object.

Synopsis

Prototype

ajuint ajFeatGetEnd (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

ajuint RETURN Feature end position

Input

thys:

(Input)

Feature object

Returns

ajuint:

Feature end position

Description

Returns the end position of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetLength

Returns the sequence length of a feature object.

Synopsis

Prototype

ajuint ajFeatGetLength (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

ajuint RETURN Feature length

Input

thys:

(Input)

Feature object

Returns

ajuint:

Feature length

Description

Returns the sequence length of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetScore

Returns the score of a feature object.

Synopsis

Prototype

float ajFeatGetScore (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

float RETURN Feature score

Input

thys:

(Input)

Feature object

Returns

float:

Feature score

Description

Returns the score of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetForward

Returns the direction of a feature object.

Synopsis

Prototype

AjBool ajFeatGetForward (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

AjBool RETURN ajTrue for a forward direction, ajFalse for reverse

Input

thys:

(Input)

Feature object

Returns

AjBool:

ajTrue for a forward direction, ajFalse for reverse

Description

Returns the direction of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetFrame

Returns the reading frame of a feature object.

Synopsis

Prototype

ajint ajFeatGetFrame (
      const AjPFeature thys
);

Type Name Read/Write Description

const AjPFeature thys Input Feature object

ajint RETURN Feature reading frame (zero for undefined)

Input

thys:

(Input)

Feature object

Returns

ajint:

Feature reading frame (zero for undefined)

Description

Returns the reading frame of a feature object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatGetTrans

Returns translation information from catenated sequence entry

Synopsis

Prototype

ajuint ajFeatGetTrans (
      const AjPStr str,
      AjPStr** cds
);

Type Name Read/Write Description

const AjPStr str Input catenated (seq->TextPtr) entry

AjPStr** cds Output array of translations

ajuint RETURN number of location lines

Input

str:

(Input)

catenated (seq->TextPtr) entry

Output

cds:

(Output)

array of translations

Returns

ajuint:

number of location lines

Description

Returns translation information from catenated sequence entry

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatTest

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

Synopsis

Prototype

void ajFeatTest (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSetDescApp

Sets the description for a feature

Synopsis

Prototype

void ajFeatSetDescApp (
      AjPFeature thys,
      const AjPStr desc
);

Type Name Read/Write Description

AjPFeature thys Modify Feature

const AjPStr desc Input Feature description (simple text)

void RETURN

Input

desc:

(Input)

Feature description (simple text)

Input & Output

thys:

(Modify)

Feature

Returns

void:

No return value

Description

Sets the description for a feature

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSetDesc

Sets the description for a feature

Synopsis

Prototype

void ajFeatSetDesc (
      AjPFeature thys,
      const AjPStr desc
);

Type Name Read/Write Description

AjPFeature thys Modify Feature

const AjPStr desc Input Feature description (simple text)

void RETURN

Input

desc:

(Input)

Feature description (simple text)

Input & Output

thys:

(Modify)

Feature

Returns

void:

No return value

Description

Sets the description for a feature

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSetScore

Sets the score for a feature

Synopsis

Prototype

void ajFeatSetScore (
      AjPFeature thys,
      float score
);

Type Name Read/Write Description

AjPFeature thys Modify Feature

float score Input Score value

void RETURN

Input

score:

(Input)

Score value

Input & Output

thys:

(Modify)

Feature

Returns

void:

No return value

Description

Sets the score for a feature

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatSetStrand

Sets the score for a feature

Synopsis

Prototype

void ajFeatSetStrand (
      AjPFeature thys,
      AjBool rev
);

Type Name Read/Write Description

AjPFeature thys Modify Feature

AjBool rev Input True if reverse strand

void RETURN

Input

rev:

(Input)

True if reverse strand

Input & Output

thys:

(Modify)

Feature

Returns

void:

No return value

Description

Sets the score for a feature

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInSetType

Sets the type for feature input

Synopsis

Prototype

AjBool ajFeattabInSetType (
      AjPFeattabIn thys,
      const AjPStr type
);

Type Name Read/Write Description

AjPFeattabIn thys Modify Feature input object

const AjPStr type Input Feature type "nucleotide" "protein"

AjBool RETURN ajTrue on success

Input

type:

(Input)

Feature type "nucleotide" "protein"

Input & Output

thys:

(Modify)

Feature input object

Returns

AjBool:

ajTrue on success

Description

Sets the type for feature input

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabInSetTypeC

Sets the type for feature input

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeattabIn thys Modify Feature input object

const char* type Input Feature type "nucleotide" "protein"

AjBool RETURN ajTrue on success

Input

type:

(Input)

Feature type "nucleotide" "protein"

Input & Output

thys:

(Modify)

Feature input object

Returns

AjBool:

ajTrue on success

Description

Sets the type for feature input

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutSetType

Sets the type for feature output

Synopsis

Prototype

AjBool ajFeattabOutSetType (
      AjPFeattabOut thys,
      const AjPStr type
);

Type Name Read/Write Description

AjPFeattabOut thys Modify Feature output object

const AjPStr type Input Feature type "nucleotide" "protein"

AjBool RETURN ajTrue on success

Input

type:

(Input)

Feature type "nucleotide" "protein"

Input & Output

thys:

(Modify)

Feature output object

Returns

AjBool:

ajTrue on success

Description

Sets the type for feature output

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattabOutSetTypeC

Sets the type for feature output

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeattabOut thys Modify Feature output object

const char* type Input Feature type "nucleotide" "protein"

AjBool RETURN ajTrue on success

Input

type:

(Input)

Feature type "nucleotide" "protein"

Input & Output

thys:

(Modify)

Feature output object

Returns

AjBool:

ajTrue on success

Description

Sets the type for feature output

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatTagSetC

Sets a feature tag value

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeature thys Modify Feature

const char* tag Input Feature tag

const AjPStr value Input Feature tag value

AjBool RETURN ajTrue is value was valid ajFalse if it was "corrceted"

Input

tag:	(Input)	Feature tag
value:	(Input)	Feature tag value

Input & Output

thys:

(Modify)

Feature

Returns

AjBool:

ajTrue is value was valid ajFalse if it was "corrceted"

Description

Sets a feature tag value

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatTagSet

Sets a feature tag value

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeature thys Modify Feature

const AjPStr tag Input Feature tag

const AjPStr value Input Feature tag value

AjBool RETURN ajTrue is value was valid ajFalse if it was "corrceted"

Input

tag:	(Input)	Feature tag
value:	(Input)	Feature tag value

Input & Output

thys:

(Modify)

Feature

Returns

AjBool:

ajTrue is value was valid ajFalse if it was "corrceted"

Description

Sets a feature tag value

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatTagAddCC

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

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeature thys Modify Feature

const char* tag Input Feature tag

const char* value Input Feature tag value

AjBool RETURN ajTrue if value was valid ajFalse if it was bad and was "corrected"

Input

tag:	(Input)	Feature tag
value:	(Input)	Feature tag value

Input & Output

thys:

(Modify)

Feature

Returns

AjBool:

ajTrue if value was valid ajFalse if it was bad and was "corrected"

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatTagAddC

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

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeature thys Modify Feature

const char* tag Input Feature tag

const AjPStr value Input Feature tag value

AjBool RETURN ajTrue if value was valid ajFalse if it was bad and was "corrected"

Input

tag:	(Input)	Feature tag
value:	(Input)	Feature tag value

Input & Output

thys:

(Modify)

Feature

Returns

AjBool:

ajTrue if value was valid ajFalse if it was bad and was "corrected"

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatTagAdd

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

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeature thys Modify Feature

const AjPStr tag Input Feature tag

const AjPStr value Input Feature tag value

AjBool RETURN ajTrue if value was valid ajFalse if it was bad and was "corrected"

Input

tag:	(Input)	Feature tag
value:	(Input)	Feature tag value

Input & Output

thys:

(Modify)

Feature

Returns

AjBool:

ajTrue if value was valid ajFalse if it was bad and was "corrected"

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableNew

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

Synopsis

Prototype

AjPFeattable ajFeattableNew (
      const AjPStr name 
);

Type Name Read/Write Description

const AjPStr name Input Name for new feature table (or NULL for unnamed)

AjPFeattable RETURN Pointer to a new (empty) feature table

Input

name:

(Input)

Name for new feature table (or NULL for unnamed)

Returns

AjPFeattable:

Pointer to a new (empty) feature table

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatUfoRead

Parses a UFO, opens an input file, and reads a feature table

Synopsis

Prototype

AjPFeattable ajFeatUfoRead (
      AjPFeattabIn featin,
      const AjPStr ufo
);

Type Name Read/Write Description

AjPFeattabIn featin Modify Feature input object

const AjPStr ufo Input UFO feature spec

AjPFeattable RETURN Feature table created, (or NULL if failed)

Input

ufo:

(Input)

UFO feature spec

Input & Output

featin:

(Modify)

Feature input object

Returns

AjPFeattable:

Feature table created, (or NULL if failed)

Description

Parses a UFO, opens an input file, and reads a feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableSetLength

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

This is needed to reverse the table correctly

Synopsis

Prototype

void ajFeattableSetLength (
      AjPFeattable thys,
      ajuint len
);

Type Name Read/Write Description

AjPFeattable thys Modify Feature table object

ajuint len Input Length

void RETURN

Input

len:

(Input)

Length

Input & Output

thys:

(Modify)

Feature table object

Returns

void:

No return value

Description

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

This is needed to reverse the table correctly

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableSetNuc

Sets the type of a feature table as nucleotide

Synopsis

Prototype

void ajFeattableSetNuc (
      AjPFeattable thys
);

Type Name Read/Write Description

AjPFeattable thys Modify Feature table object

void RETURN

Input & Output

thys:

(Modify)

Feature table object

Returns

void:

No return value

Description

Sets the type of a feature table as nucleotide

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableSetProt

Sets the type of a feature table as Protein

Synopsis

Prototype

void ajFeattableSetProt (
      AjPFeattable thys
);

Type Name Read/Write Description

AjPFeattable thys Modify Feature table object

void RETURN

Input & Output

thys:

(Modify)

Feature table object

Returns

void:

No return value

Description

Sets the type of a feature table as Protein

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableReverse

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

Synopsis

Prototype

void ajFeattableReverse (
      AjPFeattable thys
);

Type Name Read/Write Description

AjPFeattable thys Modify Feature table object

void RETURN

Input & Output

thys:

(Modify)

Feature table object

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeatReverse

Reverse one feature by reversing all positions and strand.

Synopsis

Prototype

void ajFeatReverse (
      AjPFeature thys,
      ajint ilen
);

Type Name Read/Write Description

AjPFeature thys Modify Feature object

ajint ilen Input Sequence length

void RETURN

Input

ilen:

(Input)

Sequence length

Input & Output

thys:

(Modify)

Feature object

Returns

void:

No return value

Description

Reverse one feature by reversing all positions and strand.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableSetRange

Set the begin and end range for a feature table

Synopsis

Prototype

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

Type Name Read/Write Description

AjPFeattable thys Modify Feature table object

ajint fbegin Input Begin position

ajint fend Input End position

void RETURN

Input

fbegin:	(Input)	Begin position
fend:	(Input)	End position

Input & Output

thys:

(Modify)

Feature table object

Returns

void:

No return value

Description

Set the begin and end range for a feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableNewDna

Constructor for a new DNA feature table

Synopsis

Prototype

AjPFeattable ajFeattableNewDna (
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr name Input Name for new feature table (or NULL for unnamed)

AjPFeattable RETURN Pointer to a new (empty) feature table

Input

name:

(Input)

Name for new feature table (or NULL for unnamed)

Returns

AjPFeattable:

Pointer to a new (empty) feature table

Description

Constructor for a new DNA feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableNewSeq

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

Synopsis

Prototype

AjPFeattable ajFeattableNewSeq (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object to provide the name and type

AjPFeattable RETURN Pointer to a new (empty) feature table

Input

seq:

(Input)

Sequence object to provide the name and type

Returns

AjPFeattable:

Pointer to a new (empty) feature table

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableNewProt

Constructor for a new protein feature table

Synopsis

Prototype

AjPFeattable ajFeattableNewProt (
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr name Input Name for new feature table (or NULL for unnamed)

AjPFeattable RETURN Pointer to a new (empty) feature table

Input

name:

(Input)

Name for new feature table (or NULL for unnamed)

Returns

AjPFeattable:

Pointer to a new (empty) feature table

Description

Constructor for a new protein feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableCopy

Makes a copy of a feature table.

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

Synopsis

Prototype

AjPFeattable ajFeattableCopy (
      const AjPFeattable orig
);

Type Name Read/Write Description

const AjPFeattable orig Input Original feature table

AjPFeattable RETURN Feature table copy of the original

Input

orig:

(Input)

Original feature table

Returns

AjPFeattable:

Feature table copy of the original

Description

Makes a copy of a feature table.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function ajFeattableCopyLimit

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

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

Synopsis

Prototype

AjPFeattable ajFeattableCopyLimit (
      const AjPFeattable orig,
      ajint limit
);

Type Name Read/Write Description

const AjPFeattable orig Input Original feature table

ajint limit Input Limit to number of features copied

AjPFeattable RETURN Feature table copy of the or

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

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
AjPFeature*	pthis	Delete	Pointer to the object to be deleted. The pointer is always deleted.
void		RETURN

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

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

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

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

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)

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

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

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

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

ajfeat.c

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