ajfeat.c

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.

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
);

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 3.0.0

Function ajFeattabOutFile

Returns the name of a feature output file

Synopsis

Prototype

AjPFile ajFeattabOutFile (
      const AjPFeattabOut thys
);

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 3.0.0

Function ajFeattabOutFilename

Returns the name of a feature output file

Synopsis

Prototype

AjPStr ajFeattabOutFilename (
      const AjPFeattabOut thys
);

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 3.0.0

Function ajFeattabOutIsOpen

Checks whether feature output file has already been opened

Synopsis

Prototype

AjBool ajFeattabOutIsOpen (
      const AjPFeattabOut thys
);

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 3.0.0

Function ajFeattabOutIsLocal

Checks whether feature output file has already been opened

Synopsis

Prototype

AjBool ajFeattabOutIsLocal (
      const AjPFeattabOut thys
);

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 3.0.0

Function ajFeattabOutSet

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

Synopsis

Prototype

AjBool ajFeattabOutSet (
      AjPFeattabOut thys,
      const AjPStr ufo
);

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 3.0.0

Function ajFeattabInNew

Constructor for an empty feature table input object

Synopsis

Prototype

AjPFeattabIn ajFeattabInNew (
      void
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajFeattabOutNew

Constructor for an empty feature table output object

Synopsis

Prototype

AjPFeattabOut ajFeattabOutNew (
      void
);

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 3.0.0

Function ajFeattabOutSetBasename

Sets the base output filename for feature table output

Synopsis

Prototype

void ajFeattabOutSetBasename (
      AjPFeattabOut thys,
      const AjPStr basename
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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 3.0.0

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 3.0.0

Feature Object Destructors

(Simple minded) object destruction by release of memory.

No reference counting (for now).

Function ajFeattabInDel

Destructor for a feature table input object

Synopsis

Prototype

void ajFeattabInDel (
      AjPFeattabIn* pthis
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Feature Assignments

Sets the input format for a feature table using the feature input DE object's defined format.

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
);

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 3.0.0

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
);

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 3.0.0

Function ajFeatSortByType

Sort Feature table by Type.

Synopsis

Prototype

void ajFeatSortByType (
      AjPFeattable Feattab
);

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 3.0.0

Function ajFeatSortByStart

Sort Feature table by Start position.

Synopsis

Prototype

void ajFeatSortByStart (
      AjPFeattable Feattab
);

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 3.0.0

Function ajFeatSortByEnd

Sort Feature table by End position.

Synopsis

Prototype

void ajFeatSortByEnd (
      AjPFeattable Feattab
);

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 3.0.0

Feature Table Modifiers

Function ajFeattableAdd

Method to add a new AjPFeature to a AjPFeattable

Synopsis

Prototype

void ajFeattableAdd (
      AjPFeattable thys,
      AjPFeature feature
);

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 3.0.0

Feature Object Operators

Initialize the components of a previously allocated AjPFeattable object.

Function ajFeattableClear

Clears a feature table of all features

Synopsis

Prototype

void ajFeattableClear (
      AjPFeattable thys
);

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 3.0.0

Function ajFeatOutFormatDefault

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

Synopsis

Prototype

AjBool ajFeatOutFormatDefault (
      AjPStr* pformat
);

Output

pformat:

(Output)

Default output feature format.

Returns

AjBool:

ajTrue on success.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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 3.0.0

Function ajFeattableWriteGff

Write feature table in GFF format

Synopsis

Prototype

AjBool ajFeattableWriteGff (
      const AjPFeattable Feattab,
      AjPFile file
);

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 3.0.0

Function ajFeattableWriteDdbj

Write a feature table in DDBJ format.

Synopsis

Prototype

AjBool ajFeattableWriteDdbj (
      const AjPFeattable thys,
      AjPFile file
);

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 3.0.0

Function ajFeattableWriteEmbl

Write a feature table in EMBL format.

Synopsis

Prototype

AjBool ajFeattableWriteEmbl (
      const AjPFeattable thys,
      AjPFile file
);

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 3.0.0

Function ajFeattableWriteGenbank

Write a feature table in GenBank format.

Synopsis

Prototype

AjBool ajFeattableWriteGenbank (
      const AjPFeattable thys,
      AjPFile file
);

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 3.0.0

Function ajFeattableWriteSwiss

Write a feature table in SwissProt format.

Synopsis

Prototype

AjBool ajFeattableWriteSwiss (
      const AjPFeattable thys,
      AjPFile file
);

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 3.0.0

Function ajFeattableWritePir

Write a feature table in PIR format.

Synopsis

Prototype

AjBool ajFeattableWritePir (
      const AjPFeattable thys,
      AjPFile file
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajFeattableIsNuc

Returns ajTrue if a feature table is knucleotide protein

Synopsis

Prototype

AjBool ajFeattableIsNuc (
      const AjPFeattable thys
);

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 3.0.0

Function ajFeattableIsProt

Returns ajTrue if a feature table is protein

Synopsis

Prototype

AjBool ajFeattableIsProt (
      const AjPFeattable thys
);

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 3.0.0

Function ajFeattableBegin

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

Synopsis

Prototype

ajint ajFeattableBegin (
      const AjPFeattable thys
);

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 3.0.0

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
);

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 3.0.0

Function ajFeattableLen

Returns the sequence length of a feature table

Synopsis

Prototype

ajint ajFeattableLen (
      const AjPFeattable thys
);

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 3.0.0

Function ajFeattableSize

Returns the number of features in a feature table

Synopsis

Prototype

ajint ajFeattableSize (
      const AjPFeattable thys
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajFeatGetLocs

Returns location information from catenated sequence entry

Synopsis

Prototype

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

Input

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

Output

cds:

(Output)

array of locations

Returns

ajint:

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 3.0.0

Function ajFeatGetNote

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

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 3.0.0

Function ajFeatGetNoteC

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

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 3.0.0

Function ajFeatGetNoteCI

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

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 3.0.0

Function ajFeatGetNoteI

Finds a named note tag (with a * prefix)

Synopsis

Prototype

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

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 3.0.0

Function ajFeatGetTag

Returns the nth value of a named feature tag.

Synopsis

Prototype

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

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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 3.0.0

Function ajFeatGetSource

Returns the source name of a feature object.

Synopsis

Prototype

const AjPStr ajFeatGetSource (
      const AjPFeature thys
);

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 3.0.0

Function ajFeatGetStart

Returns the start position of a feature object.

Synopsis

Prototype

ajint ajFeatGetStart (
      const AjPFeature thys
);

Input

thys:

(Input)

Feature object

Returns

ajint:

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 3.0.0

Function ajFeatGetStrand

Returns the strand of a feature object.

Synopsis

Prototype

char ajFeatGetStrand (
      const AjPFeature thys
);

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 3.0.0

Function ajFeatGetEnd

Returns the end position of a feature object.

Synopsis

Prototype

ajint ajFeatGetEnd (
      const AjPFeature thys
);

Input

thys:

(Input)

Feature object

Returns

ajint:

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 3.0.0

Function ajFeatGetLength

Returns the sequence length of a feature object.

Synopsis

Prototype

ajint ajFeatGetLength (
      const AjPFeature thys
);

Input

thys:

(Input)

Feature object

Returns

ajint:

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 3.0.0

Function ajFeatGetScore

Returns the score of a feature object.

Synopsis

Prototype

float ajFeatGetScore (
      const AjPFeature thys
);

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 3.0.0

Function ajFeatGetForward

Returns the direction of a feature object.

Synopsis

Prototype

AjBool ajFeatGetForward (
      const AjPFeature thys
);

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 3.0.0

Function ajFeatGetFrame

Returns the reading frame of a feature object.

Synopsis

Prototype

ajint ajFeatGetFrame (
      const AjPFeature thys
);

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 3.0.0

Function ajFeatGetTrans

Returns translation information from catenated sequence entry

Synopsis

Prototype

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

Input

str:

(Input)

catenated (seq->TextPtr) entry

Output

cds:

(Output)

array of translations

Returns

ajint:

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 3.0.0

Function ajFeatTest

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

Synopsis

Prototype

void ajFeatTest (
      void
);

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 3.0.0

Function ajFeatSetDescApp

Sets the description for a feature

Synopsis

Prototype

void ajFeatSetDescApp (
      AjPFeature thys,
      const AjPStr desc
);

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 3.0.0

Function ajFeatSetDesc

Sets the description for a feature

Synopsis

Prototype

void ajFeatSetDesc (
      AjPFeature thys,
      const AjPStr desc
);

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 3.0.0

Function ajFeatSetScore

Sets the score for a feature

Synopsis

Prototype

void ajFeatSetScore (
      AjPFeature thys,
      float score
);

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 3.0.0

Function ajFeatSetStrand

Sets the score for a feature

Synopsis

Prototype

void ajFeatSetStrand (
      AjPFeature thys,
      AjBool rev
);

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 3.0.0

Function ajFeattabInSetType

Sets the type for feature input

Synopsis

Prototype

AjBool ajFeattabInSetType (
      AjPFeattabIn thys,
      const AjPStr type
);

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 3.0.0

Function ajFeattabInSetTypeC

Sets the type for feature input

Synopsis

Prototype

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

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 3.0.0

Function ajFeattabOutSetType

Sets the type for feature output

Synopsis

Prototype

AjBool ajFeattabOutSetType (
      AjPFeattabOut thys,
      const AjPStr type
);

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 3.0.0

Function ajFeattabOutSetTypeC

Sets the type for feature output

Synopsis

Prototype

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

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 3.0.0

Function ajFeatTagSetC

Sets a feature tag value

Synopsis

Prototype

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

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 3.0.0

Function ajFeatTagSet

Sets a feature tag value

Synopsis

Prototype

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

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

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
);

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 3.0.0

Function ajFeattableNew

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

Synopsis

Prototype

AjPFeattable ajFeattableNew (
      const AjPStr name 
);

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 3.0.0

Function ajFeatUfoRead

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

Synopsis

Prototype

AjPFeattable ajFeatUfoRead (
      AjPFeattabIn featin,
      const AjPStr ufo
);

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 3.0.0

Function ajFeattableSetNuc

Sets the type of a feature table as nucleotide

Synopsis

Prototype

void ajFeattableSetNuc (
      AjPFeattable thys
);

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 3.0.0

Function ajFeattableSetProt

Sets the type of a feature table as Protein

Synopsis

Prototype

void ajFeattableSetProt (
      AjPFeattable thys
);

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 3.0.0

Function ajFeattableReverse

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

Synopsis

Prototype

void ajFeattableReverse (
      AjPFeattable thys
);

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 3.0.0

Function ajFeatReverse

Reverse one feature by reversing all positions and strand.

Synopsis

Prototype

void ajFeatReverse (
      AjPFeature thys,
      ajint ilen
);

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 3.0.0

Function ajFeattableSetRange

Set the begin and end range for a feature table

Synopsis

Prototype

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

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 3.0.0

Function ajFeattableNewDna

Constructor for a new DNA feature table

Synopsis

Prototype

AjPFeattable ajFeattableNewDna (
      const AjPStr name
);

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 3.0.0

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
);

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 3.0.0

Function ajFeattableNewProt

Constructor for a new protein feature table

Synopsis

Prototype

AjPFeattable ajFeattableNewProt (
      const AjPStr name
);

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 3.0.0

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
);

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 3.0.0

Function ajFeatCopy

Makes a copy of a feature.

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

Synopsis

Prototype

AjPFeature ajFeatCopy (
      const AjPFeature orig
);

Input

orig:

(Input)

Original feature

Returns

AjPFeature:

Feature copy of the original

Description

Makes a copy of a feature.

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 3.0.0

Function ajFeatTrace

Traces (to the debug file) a feature object

Synopsis

Prototype

void ajFeatTrace (
      const AjPFeature thys
);

Input

thys:

(Input)

Feature

Returns

void:

No return value

Description

Traces (to the debug file) a feature object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatTagTrace

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

Synopsis

Prototype

void ajFeatTagTrace (
      const AjPFeature thys
);

Input

thys:

(Input)

Feature

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatTagIter

Returns an iterator over all feature tag-value pairs

Synopsis

Prototype

AjIList ajFeatTagIter (
      const AjPFeature thys
);

Input

thys:

(Input)

Feature

Returns

AjIList:

List iterator

Description

Returns an iterator over all feature tag-value pairs

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatTagval

Returns the tag-value pairs of a feature object

Synopsis

Prototype

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

Output

tagnam:	(Output)	Tag name
tagval:	(Output)	Tag val

Input & Output

iter:

(Modify)

List iterator from ajFeatTagIter

Returns

AjBool:

ajTrue if another tag-value pair was returned

Description

Returns the tag-value pairs of a feature object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeattableTrace

Traces (to the debug file) a complete feature table

Synopsis

Prototype

void ajFeattableTrace (
      const AjPFeattable thys
);

Input

thys:

(Input)

Feature table

Returns

void:

No return value

Description

Traces (to the debug file) a complete feature table

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatExit

Prints a summary of file usage with debug calls

Cleans up feature table internal memory

Synopsis

Prototype

void ajFeatExit (
      void
);

Returns

void:

No return value

Description

Prints a summary of file usage with debug calls

Cleans up feature table internal memory

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatUnused

Dummy function to prevent compiler warnings

Synopsis

Prototype

void ajFeatUnused (
      void
);

Returns

void:

No return value

Description

Dummy function to prevent compiler warnings

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatIsLocal

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

Synopsis

Prototype

AjBool ajFeatIsLocal (
      const AjPFeature gf
);

Input

gf:

(Input)

Feature

Returns

AjBool:

ajTrue on success

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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.)

Synopsis

Prototype

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

Input

gf:	(Input)	Feature
start:	(Input)	start of range
end:	(Input)	end of range

Returns

AjBool:

ajTrue on success

Description

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.)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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

Synopsis

Prototype

AjBool ajFeatIsChild (
      const AjPFeature gf
);

Input

gf:

(Input)

Feature

Returns

AjBool:

Returns AJTRUE if it is a child, AJFALSE if it is not a child

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatIsMultiple

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

Synopsis

Prototype

AjBool ajFeatIsMultiple (
      const AjPFeature gf
);

Input

gf:

(Input)

Feature

Returns

AjBool:

Returns AJTRUE if it is a member

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatIsCompMult

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

Synopsis

Prototype

AjBool ajFeatIsCompMult (
      const AjPFeature gf
);

Input

gf:

(Input)

Feature

Returns

AjBool:

Returns AJTRUE if it is a complemented multiple

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeattabOutDel

Destructor for a feature table output object

Synopsis

Prototype

void ajFeattabOutDel (
      AjPFeattabOut* thys
);

Output

thys:

(Delete)

feature format

Returns

void:

No return value

Description

Destructor for a feature table output object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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.

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

Synopsis

Prototype

ajint ajFeattablePos (
      const AjPFeattable thys,
      ajint ipos
);

Input

thys:	(Input)	Target feature table.
ipos:	(Input)	Position.

Returns

ajint:

string position between 1 and length.

Description

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.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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.

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

Synopsis

Prototype

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

Input

thys:	(Input)	Target feature table.
imin:	(Input)	Start position.
ipos:	(Input)	Position.

Returns

ajint:

string position between 1 and length.

Description

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.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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.

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

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

Synopsis

Prototype

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

Input

ilen:	(Input)	maximum length.
imin:	(Input)	Start position.
ipos:	(Input)	Position.

Returns

ajint:

string position between 1 and length.

Description

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

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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeattableTrimOff

Trim a feature table using the Begin and Ends.

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

Synopsis

Prototype

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

Input

ioffset:	(Input)	Offset from start of sequence
ilen:	(Input)	Length of sequence

Input & Output

thys:

(Modify)

Target feature table.

Returns

AjBool:

AjTrue returned if successful.

Description

Trim a feature table using the Begin and Ends.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatTrimOffRange

Trim a feature table using the Begin and Ends.

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

Synopsis

Prototype

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

Input

ioffset:	(Input)	Offset from start of sequence
begin:	(Input)	Range start of sequence
end:	(Input)	range end of sequence
dobegin:	(Input)	Reset begin
doend:	(Input)	Reset end

Input & Output

ft:

(Modify)

Target feature

Returns

AjBool:

AjTrue returned if successful.

Description

Trim a feature table using the Begin and Ends.

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatDefName

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

Synopsis

Prototype

void ajFeatDefName (
      AjPFeattable thys,
      const AjPStr setname
);

Input

setname:

(Input)

Name set by caller

Output

thys:

(Output)

Feature table

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajFeatPrintFormat

Reports the internal data structures

Synopsis

Prototype

void ajFeatPrintFormat (
      AjPFile outf,
      AjBool full
);

Input

full:

(Input)

Full report (usually ajFalse)

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the internal data structures

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

ajfeat.c

Synopsis

Prototype

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

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Synopsis

Prototype

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis