ajfeat.c


Section: Feature Object Constructors

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

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

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

Functions: ajFeatNew ajFeatNewSub ajFeatNewII ajFeatNewIISub ajFeatNewIIRev ajFeatNewIIRevSub ajFeatNewProt ajFeatNewProtSub ajFeatNewProtFlags ajFeatNewProtFlagsSub ajFeatCompByStart ajFeatCompByEnd ajFeatCompByGroup ajFeatCompByType ajFeatNewNuc ajFeatNewNucSub ajFeatNewNucFlags ajFeatNewNucFlagsSub


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
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
charstrandInputStrand of the feature
ajintframeInputFrame of the feature
AjPFeature RETURNnewly 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!

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewSub

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
charstrandInputStrand of the feature
ajintframeInputFrame of the feature
AjPFeature RETURNnewly 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
parent:(Modify)Parent feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
AjPFeature RETURNnewly 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!

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewIISub

Simple constructor with only start and end positions

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
AjPFeature RETURNnewly 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
parent:(Modify)Parent 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!

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
AjPFeature RETURNnewly 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, sets feature to be on the reverse strand

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewIIRevSub

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
AjPFeature RETURNnewly 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
parent:(Modify)Parent 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!

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
AjPFeature RETURNnewly 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
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!

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewProtSub

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
AjPFeature RETURNnewly 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
Input & Output
thys:(Modify)Pointer to the ajFeattable which will own the feature
parent:(Modify)Parent feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewProtFlags

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
ajuintflagsInputflags.
AjPFeature RETURNnewly 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
flags:(Input)flags.
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!

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewProtFlagsSub

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
ajuintflagsInputflags.
AjPFeature RETURNnewly 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
flags:(Input)flags.
Input & Output
thys:(Modify)Pointer to the ajFeattable which will own the feature
parent:(Modify)Parent feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatCompByStart

Compare two features by their start.

Synopsis

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

TypeNameRead/WriteDescription
const void*aInputfeature
const void*bInputanother feature
ajint RETURN-1 if a is less than b, 0 if a is equal to b else +1.

Input
a:(Input)feature
b:(Input)another feature
Returns
ajint:-1 if a is less than b, 0 if a is equal to b else +1.

Description

Compare two features by their start.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatCompByEnd

Compare two features by their end.

Synopsis

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

TypeNameRead/WriteDescription
const void*aInputfeature
const void*bInputanother feature
ajint RETURN-1 if a is less than b, 0 if a is equal to b else +1.

Input
a:(Input)feature
b:(Input)another feature
Returns
ajint:-1 if a is less than b, 0 if a is equal to b else +1.

Description

Compare two features by their end.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatCompByGroup

Compare two features by their group and exon numbers

Synopsis

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

TypeNameRead/WriteDescription
const void*aInputfeature
const void*bInputanother feature
ajint RETURN-1 if a is less than b, 0 if a is equal to b else +1.

Input
a:(Input)feature
b:(Input)another feature
Returns
ajint:-1 if a is less than b, 0 if a is equal to b else +1.

Description

Compare two features by their group and exon numbers

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatCompByType

Compare two features by their type (key).

Synopsis

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

TypeNameRead/WriteDescription
const void*aInputfeature
const void*bInputanother feature
ajint RETURN-1 if a is less than b, 0 if a is equal to b else +1.

Input
a:(Input)feature
b:(Input)another feature
Returns
ajint:-1 if a is less than b, 0 if a is equal to b else +1.

Description

Compare two features by their type (key).

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewNuc

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
charstrandInputStrand of the feature
ajintframeInputFrame of the feature
ajintexonInputexon number (0 for default value)
ajintStart2Input2nd Start position of the feature
ajintEnd2Input2nd End position of the feature
const AjPStrentryidInputEntry ID for location in another entry
const AjPStrlabelInputLabel for location (non-numeric)
AjPFeature RETURNnewly 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
exon:(Input)exon number (0 for default value)
Start2:(Input)2nd Start position of the feature
End2:(Input)2nd End position of the feature
entryid:(Input)Entry ID for location in another entry
label:(Input)Label for location (non-numeric)
Input & Output
thys:(Modify)Pointer to the ajFeattable which will own the feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewNucSub

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
charstrandInputStrand of the feature
ajintframeInputFrame of the feature
ajintexonInputexon number (0 for default value)
ajintStart2Input2nd Start position of the feature
ajintEnd2Input2nd End position of the feature
const AjPStrentryidInputEntry ID for location in another entry
const AjPStrlabelInputLabel for location (non-numeric)
AjPFeature RETURNnewly 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
exon:(Input)exon number (0 for default value)
Start2:(Input)2nd Start position of the feature
End2:(Input)2nd End position of the feature
entryid:(Input)Entry ID for location in another entry
label:(Input)Label for location (non-numeric)
Input & Output
thys:(Modify)Pointer to the ajFeattable which will own the feature
parent:(Modify)Parent feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewNucFlags

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
charstrandInputStrand of the feature
ajintframeInputFrame of the feature
ajintexonInputexon number (0 for default value)
ajintStart2Input2nd Start position of the feature
ajintEnd2Input2nd End position of the feature
const AjPStrentryidInputEntry ID for location in another entry
const AjPStrlabelInputLabel for location (non-numeric)
ajuintflagsInputflags.
AjPFeature RETURNnewly 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
exon:(Input)exon number (0 for default value)
Start2:(Input)2nd Start position of the feature
End2:(Input)2nd End position of the feature
entryid:(Input)Entry ID for location in another entry
label:(Input)Label for location (non-numeric)
flags:(Input)flags.
Input & Output
thys:(Modify)Pointer to the ajFeattable which will own the feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewNucFlagsSub

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyPointer to the ajFeattable which will own the feature
AjPFeatureparentModifyParent feature
const AjPStrsourceInputAnalysis basis for feature
const AjPStrtypeInputType of feature (e.g. exon)
ajintStartInputStart position of the feature
ajintEndInputEnd position of the feature
floatscoreInputAnalysis score for the feature
charstrandInputStrand of the feature
ajintframeInputFrame of the feature
ajintexonInputexon number (0 for default value)
ajintStart2Input2nd Start position of the feature
ajintEnd2Input2nd End position of the feature
const AjPStrentryidInputEntry ID for location in another entry
const AjPStrlabelInputLabel for location (non-numeric)
ajuintflagsInputflags.
AjPFeature RETURNnewly 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
exon:(Input)exon number (0 for default value)
Start2:(Input)2nd Start position of the feature
End2:(Input)2nd End position of the feature
entryid:(Input)Entry ID for location in another entry
label:(Input)Label for location (non-numeric)
flags:(Input)flags.
Input & Output
thys:(Modify)Pointer to the ajFeattable which will own the feature
parent:(Modify)Parent feature
Returns
AjPFeature:newly allocated feature object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Feature Object Destructors

(Simple minded) object destruction by release of memory.

No reference counting (for now).

Functions: ajFeattableDel ajFeatDel


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
);

TypeNameRead/WriteDescription
AjPFeattable*pthisDeletePointer 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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeature*pthisDeletePointer 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Feature Assignments

Functions: ajFeatSortByType ajFeatSortByStart ajFeatSortByEnd


Function ajFeatSortByType

Sort Feature table by Type.

Synopsis

Prototype
void ajFeatSortByType (
      AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattableFeattabModifyFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSortByStart

Sort Feature table by Start position.

Synopsis

Prototype
void ajFeatSortByStart (
      AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattableFeattabModifyFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSortByEnd

Sort Feature table by End position.

Synopsis

Prototype
void ajFeatSortByEnd (
      AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattableFeattabModifyFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyThe feature table
AjPFeaturefeatureModifyFeature 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

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Feature Object Operators

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

Functions: ajFeattableClear ajFeatTypeGetCategory ajFeattableGetEntry ajFeattableGetQryC ajFeattableGetQryS ajFeattableGetTypeC ajFeattableGetTypeS ajFeattableGetXrefs ajFeatframeGetFrame ajFeatframeGetFrameNuc ajFeatstrandGetStrand ajFeattableIsNuc ajFeattableIsProt ajFeattableGetBegin ajFeattableGetEnd ajFeattableGetLen ajFeattableGetName ajFeattableGetSize ajFeatGetFlags ajFeatGetSeq ajFeatGetSeqJoin ajFeatGetRemoteseq ajFeatGetXrefs ajFeatLocMark ajFeatGetNoteC ajFeatGetNoteCI ajFeatGetNoteSI ajFeatGetNoteS ajFeatGetTagC ajFeatGetTagS ajFeatGetType ajFeatGetSource ajFeatGetStart ajFeatGetStrand ajFeatGetEnd ajFeatGetLength ajFeatGetScore ajFeatGetForward ajFeatGetFrame ajFeatGetTranslation ajFeatTest ajFeatVocabGetTags ajFeatVocabGetTagsNuc ajFeatVocabGetTagsProt ajFeatVocabGetTypes ajFeatVocabGetTypesNuc ajFeatVocabGetTypesProt ajFeatVocabInit ajFeatVocabInitNuc ajFeatVocabInitProt ajFeatSetDescApp ajFeatSetDesc ajFeatSetSource ajFeatSetScore ajFeatSetStrand ajFeatTagSetC ajFeatTagSet ajFeattagSpecialGff2 ajFeattagSpecialGff3 ajFeatTagAddCC ajFeatTagAddC ajFeatTagAdd ajFeattagSpecial ajFeattableNew ajFeattableSetDefname ajFeattableSetLength ajFeattableSetNuc ajFeattableSetProt ajFeattableSetRange ajFeattableReverse ajFeatReverse ajFeattableNewDna ajFeattableNewSeq ajFeattableNewProt ajFeatGfftagAddC ajFeatGfftagAdd ajFeattableNewFtable ajFeattableNewFtableLimit ajFeatNewFeat ajFeatTrace ajFeatTagTrace ajFeatGfftagsNew ajFeatGfftagsDel ajFeatGetGfftags ajFeatGetParent ajFeatTagIter ajFeatSubIter ajFeatTagval ajFeattableTrace ajFeatTypeNuc ajFeatTypeProt ajFeattypeGetExternal ajFeattypeGetInternal ajFeattypeGetInternalEmbl ajFeattypeGetInternalNuc ajFeattypeGetInternalPir ajFeattypeGetInternalProt ajFeattypeGetInternalRefseqp ajFeattagGetNameC ajFeattagGetNameS ajFeattagFormat ajFeattagGetLimit ajFeatUnused ajFeatTypeIsCds ajFeatTypeMatchC ajFeatTypeMatchS ajFeatTypeMatchWildS ajFeatIsLocal ajFeatIsLocalRange ajFeatIsChild ajFeatIsMultiple ajFeatIsCompMult ajFeattablePos ajFeattablePosI ajFeattablePosII ajFeattableTrimOff ajFeattableTrim ajFeatTrimOffRange ajFeattagIsNote ajFeatExit ajFeatWarn


Function ajFeattableClear

Clears a feature table of all features

Synopsis

Prototype
void ajFeattableClear (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table
void RETURN

Input & Output
thys:(Modify)Feature table
Returns
void:No return value

Description

Clears a feature table of all features

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeGetCategory

returns the category name for a feature type

Used to identify category for DASGFF output

Synopsis

Prototype
const AjPStr ajFeatTypeGetCategory (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputFeature type
const AjPStr RETURNFeature category

Input
type:(Input)Feature type
Returns
const AjPStr:Feature category

Description

returns the category name for a feature type

Used to identify category for DASGFF output

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetEntry

Return the full text

Synopsis

Prototype
const AjPStr ajFeattableGetEntry (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table object
const AjPStr RETURNReturned full text

Input
thys:(Input)Feature table object
Returns
const AjPStr:Returned full text

Description

Return the full text

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetQryC

Returns the query string of a feature table data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype
const char* ajFeattableGetQryC (
      const AjPFeattable ftable
);

TypeNameRead/WriteDescription
const AjPFeattableftableInputFeature table data object.
const char* RETURNQuery as a character string.

Input
ftable:(Input)Feature table data object.
Returns
const char*:Query as a character string.

Description

Returns the query string of a feature table data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetQryS

Returns the query string of a feature table data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype
const AjPStr ajFeattableGetQryS (
      const AjPFeattable ftable
);

TypeNameRead/WriteDescription
const AjPFeattableftableInputFeature table data object.
const AjPStr RETURNQuery as a string.

Input
ftable:(Input)Feature table data object.
Returns
const AjPStr:Query as a string.

Description

Returns the query string of a feature table data object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetTypeC

Returns the name of a feature table object. This is a copy of the pointer to the name, and is still owned by the feature table and is not to be destroyed.

Synopsis

Prototype
const char* ajFeattableGetTypeC (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
const char* RETURNFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
const AjPStr RETURNFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetXrefs

Returns all cross-references from a feature table

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
AjPList*PxreflistModifyList of sequence cross-reference objects
ajuint*PtaxidOutputTaxon ID
AjBool RETURNTrue on success

Input
thys:(Input)Feature table
Output
Ptaxid:(Output)Taxon ID
Input & Output
Pxreflist:(Modify)List of sequence cross-reference objects
Returns
AjBool:True on success

Description

Returns all cross-references from a feature table

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatframeGetFrame

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

Synopsis

Prototype
char ajFeatframeGetFrame (
      ajint frame
);

TypeNameRead/WriteDescription
ajintframeInputFeature frame number
char RETURNcharacter for this frame in GFF

Input
frame:(Input)Feature frame number
Returns
char:character for this frame in GFF

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatframeGetFrameNuc

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

Synopsis

Prototype
char ajFeatframeGetFrameNuc (
      ajint frame
);

TypeNameRead/WriteDescription
ajintframeInputFeature frame number
char RETURNcharacter for this frame in GFF

Input
frame:(Input)Feature frame number
Returns
char:character for this frame in GFF

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatstrandGetStrand

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

Synopsis

Prototype
char ajFeatstrandGetStrand (
      ajint strand
);

TypeNameRead/WriteDescription
ajintstrandInputStrand
char RETURNGFF character for this strand.

Input
strand:(Input)Strand
Returns
char:GFF character for this strand.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableIsNuc

Returns ajTrue if a feature table is nucleotide

Synopsis

Prototype
AjBool ajFeattableIsNuc (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
AjBool RETURNajTrue 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 nucleotide

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableIsProt

Returns ajTrue if a feature table is protein

Synopsis

Prototype
AjBool ajFeattableIsProt (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
AjBool RETURNajTrue 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetBegin

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

Synopsis

Prototype
ajint ajFeattableGetBegin (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputfeature table object
ajint RETURNStart 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetEnd

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

Synopsis

Prototype
ajint ajFeattableGetEnd (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputfeature table object
ajint RETURNEnd 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetLen

Returns the sequence length of a feature table

Synopsis

Prototype
ajint ajFeattableGetLen (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
ajint RETURNLength 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
const AjPStr RETURNFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableGetSize

Returns the size of a feature table object.

Synopsis

Prototype
ajuint ajFeattableGetSize (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
ajuint RETURNFeature table size.

Input
thys:(Input)Feature table
Returns
ajuint:Feature table size.

Description

Returns the size of a feature table object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetFlags

Returns the sequence matching a feature. For multiple location features (joins in an EMBL/GenBank feature table) the full feature table is used to find all exons.

The database name is used to retrieve sequences from other entries

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjPStr*PflagstrModifySequence for this feature
AjBool RETURNTrue on success

Input
thys:(Input)Feature
Input & Output
Pflagstr:(Modify)Sequence for this feature
Returns
AjBool:True on success

Description

Returns the sequence matching a feature. For multiple location features (joins in an EMBL/GenBank feature table) the full feature table is used to find all exons.

The database name is used to retrieve sequences from other entries

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetSeq

Returns the sequence matching a feature.

The database name is used to retrieve sequences from other entries

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
const AjPSeqseqInputSequence for the current feature table
AjPStr*PseqstrModifySequence for this feature
AjBool RETURNTrue on success

Input
thys:(Input)Feature
seq:(Input)Sequence for the current feature table
Input & Output
Pseqstr:(Modify)Sequence for this feature
Returns
AjBool:True on success

Description

Returns the sequence matching a feature.

The database name is used to retrieve sequences from other entries

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetSeqJoin

Returns the sequence matching a feature. For multiple location features (joins in an EMBL/GenBank feature table) the full feature table is used to find all exons.

The database name is used to retrieve sequences from other entries

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
const AjPSeqseqInputSequence for the current feature table
AjPStr*PseqstrModifySequence for this feature
AjBool RETURNTrue on success

Input
thys:(Input)Feature
seq:(Input)Sequence for the current feature table
Input & Output
Pseqstr:(Modify)Sequence for this feature
Returns
AjBool:True on success

Description

Returns the sequence matching a feature. For multiple location features (joins in an EMBL/GenBank feature table) the full feature table is used to find all exons.

The database name is used to retrieve sequences from other entries

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetRemoteseq

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
const AjPStrusaInputusa of query
AjPSeqseqModifySequence object for results
AjBool RETURNTrue on success

Input
thys:(Input)Feature
usa:(Input)usa of query
Input & Output
seq:(Modify)Sequence object for results
Returns
AjBool:True on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetXrefs

Returns all cross-references from a feature

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjPList*PxreflistModifyList of sequence cross-reference objects
AjBool RETURNTrue on success

Input
thys:(Input)Feature
Input & Output
Pxreflist:(Modify)List of sequence cross-reference objects
Returns
AjBool:True on success

Description

Returns all cross-references from a feature

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatLocMark

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
const AjPFeattabletableInputFeature table
AjPStr*PseqstrModifySequence to be marked in lower case
AjBool RETURNtrue on success

Input
thys:(Input)Feature
table:(Input)Feature table
Input & Output
Pseqstr:(Modify)Sequence to be marked in lower case
Returns
AjBool:true on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetNoteC

Finds a named note tag (with a * prefix)

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const char*nameInputTag name
AjPStr*valOutputTag value (if found)
AjBool RETURNajTrue 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)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetNoteCI

Finds a named note tag (with a * prefix)

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const char*nameInputTag name
ajintcountInputTag count: zero for any, 1 for first, 2 for second
AjPStr*valOutputTag value (if found)
AjBool RETURNajTrue 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)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetNoteSI

Finds a named note tag (with a * prefix)

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStrnameInputTag name
ajintcountInputTag count: zero for any, 1 for first, 2 for second
AjPStr*valOutputTag value (if found)
AjBool RETURNajTrue 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)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetNoteS

Finds a named note tag (with a * prefix)

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStrnameInputTag name
AjPStr*valOutputTag value (if found)
AjBool RETURNajTrue 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)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetTagC

Returns the nth value of a named feature tag.

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const char*tnameInputTag name
ajintnumInputTag number
AjPStr*PvalOutputTag value (if found)
AjBool RETURNajTrue on success (feature tag found)

Input
thys:(Input)Feature object
tname:(Input)Tag name
num:(Input)Tag number
Output
Pval:(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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetTagS

Returns the nth value of a named feature tag.

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStrnameInputTag name
ajintnumInputTag number
AjPStr*valOutputTag value (if found)
AjBool RETURNajTrue 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStr RETURNFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetSource

Returns the source name of a feature object.

Synopsis

Prototype
const AjPStr ajFeatGetSource (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStr RETURNFeature source name

Input
thys:(Input)Feature object
Returns
const AjPStr:Feature source name

Description

Returns the source name of a feature object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetStart

Returns the start position of a feature object.

Synopsis

Prototype
ajuint ajFeatGetStart (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajuint RETURNFeature start position

Input
thys:(Input)Feature object
Returns
ajuint:Feature start position

Description

Returns the start position of a feature object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetStrand

Returns the strand of a feature object.

Synopsis

Prototype
char ajFeatGetStrand (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
char RETURNFeature strand code

Input
thys:(Input)Feature object
Returns
char:Feature strand code

Description

Returns the strand of a feature object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetEnd

Returns the end position of a feature object.

Synopsis

Prototype
ajuint ajFeatGetEnd (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajuint RETURNFeature end position

Input
thys:(Input)Feature object
Returns
ajuint:Feature end position

Description

Returns the end position of a feature object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetLength

Returns the sequence length of a feature object.

Synopsis

Prototype
ajuint ajFeatGetLength (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajuint RETURNFeature length

Input
thys:(Input)Feature object
Returns
ajuint:Feature length

Description

Returns the sequence length of a feature object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetScore

Returns the score of a feature object.

Synopsis

Prototype
float ajFeatGetScore (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
float RETURNFeature score

Input
thys:(Input)Feature object
Returns
float:Feature score

Description

Returns the score of a feature object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetForward

Returns the direction of a feature object.

Synopsis

Prototype
AjBool ajFeatGetForward (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
AjBool RETURNajTrue 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetFrame

Returns the reading frame of a feature object.

Synopsis

Prototype
ajint ajFeatGetFrame (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajint RETURNFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetTranslation

Returns translation tag value

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjPStr*PtransOutputTranslations
AjBool RETURNTrue if translation tag was found

Input
thys:(Input)Feature
Output
Ptrans:(Output)Translations
Returns
AjBool:True if translation tag was found

Description

Returns translation tag value

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTest

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

Synopsis

Prototype
void ajFeatTest (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabGetTags

Returns tags table for a named feature format

Synopsis

Prototype
const AjPTable ajFeatVocabGetTags (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNTags table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Tags table on success NULL on failure

Description

Returns tags table for a named feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabGetTagsNuc

Returns tags table for a named nucleotide feature format

Synopsis

Prototype
const AjPTable ajFeatVocabGetTagsNuc (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNTags table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Tags table on success NULL on failure

Description

Returns tags table for a named nucleotide feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabGetTagsProt

Returns tags table for a named protein feature format

Synopsis

Prototype
const AjPTable ajFeatVocabGetTagsProt (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNTags table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Tags table on success NULL on failure

Description

Returns tags table for a named protein feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabGetTypes

Returns types table for a named feature format

Synopsis

Prototype
const AjPTable ajFeatVocabGetTypes (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNType table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Type table on success NULL on failure

Description

Returns types table for a named feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabGetTypesNuc

Returns types table for a named nucleotide feature format

Synopsis

Prototype
const AjPTable ajFeatVocabGetTypesNuc (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNType table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Type table on success NULL on failure

Description

Returns types table for a named nucleotide feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabGetTypesProt

Returns types table for a named protein feature format

Synopsis

Prototype
const AjPTable ajFeatVocabGetTypesProt (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNType table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Type table on success NULL on failure

Description

Returns types table for a named protein feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabInit

Initialises feature table internals for a named feature format

Synopsis

Prototype
const AjPTable ajFeatVocabInit (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNType table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Type table on success NULL on failure

Description

Initialises feature table internals for a named feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabInitNuc

Initialises feature table internals for a named feature format

Synopsis

Prototype
const AjPTable ajFeatVocabInitNuc (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNType table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Type table on success NULL on failure

Description

Initialises feature table internals for a named feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatVocabInitProt

Initialises feature table internals for a named feature format

Synopsis

Prototype
const AjPTable ajFeatVocabInitProt (
      const char* name
);

TypeNameRead/WriteDescription
const char*nameInputFeature format name
const AjPTable RETURNType table on success NULL on failure

Input
name:(Input)Feature format name
Returns
const AjPTable:Type table on success NULL on failure

Description

Initialises feature table internals for a named feature format

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSetDescApp

Sets the description for a feature

Synopsis

Prototype
void ajFeatSetDescApp (
      AjPFeature thys,
      const AjPStr desc
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrdescInputFeature 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSetDesc

Sets the description for a feature

Synopsis

Prototype
void ajFeatSetDesc (
      AjPFeature thys,
      const AjPStr desc
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrdescInputFeature 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSetSource

Sets the source for a feature

Synopsis

Prototype
void ajFeatSetSource (
      AjPFeature thys,
      const AjPStr source
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrsourceInputFeature source
void RETURN

Input
source:(Input)Feature source
Input & Output
thys:(Modify)Feature
Returns
void:No return value

Description

Sets the source for a feature

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSetScore

Sets the score for a feature

Synopsis

Prototype
void ajFeatSetScore (
      AjPFeature thys,
      float score
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
floatscoreInputScore 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSetStrand

Sets the strand for a feature

Synopsis

Prototype
void ajFeatSetStrand (
      AjPFeature thys,
      AjBool rev
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
AjBoolrevInputTrue 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 strand for a feature

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTagSetC

Sets a feature tag value

Synopsis

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

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const char*tagInputFeature tag
const AjPStrvalueInputFeature tag value
AjBool RETURNajTrue is value was valid ajFalse if it was "corrected"

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 "corrected"

Description

Sets a feature tag value

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTagSet

Sets a feature tag value

Synopsis

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

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrtagInputFeature tag
const AjPStrvalueInputFeature tag value
AjBool RETURNajTrue is value was valid ajFalse if it was "corrected"

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 "corrected"

Description

Sets a feature tag value

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagSpecialGff2

Special processing for known GFF tags

This function will be very similar to featTagSpecial, with scope for future GFF-specific extensions

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrtagInputoriginal tag name
AjPStr*pvalModifytag value
AjBool RETURNajTrue on success

Input
tag:(Input)original tag name
Input & Output
pval:(Modify)tag value
Returns
AjBool:ajTrue on success

Description

Special processing for known GFF tags

This function will be very similar to featTagSpecial, with scope for future GFF-specific extensions

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagSpecialGff3

Special processing for known GFF3 tags

This function will be very similar to featTagSpecial, with scope for future GFF3-specific extensions

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrtagInputoriginal tag name
AjPStr*pvalModifytag value
AjBool RETURNajTrue on success

Input
tag:(Input)original tag name
Input & Output
pval:(Modify)tag value
Returns
AjBool:ajTrue on success

Description

Special processing for known GFF3 tags

This function will be very similar to featTagSpecial, with scope for future GFF3-specific extensions

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const char*tagInputFeature tag
const char*valueInputFeature tag value
AjBool RETURNajTrue 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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const char*tagInputFeature tag
const AjPStrvalueInputFeature tag value
AjBool RETURNajTrue 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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrtagInputFeature tag
const AjPStrvalueInputFeature tag value
AjBool RETURNajTrue 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagSpecial

Special processing for known internal (EMBL) tags

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrtagInputoriginal tag name
AjPStr*pvalModifyparameter value
AjBool RETURNajTrue on success

Input
tag:(Input)original tag name
Input & Output
pval:(Modify)parameter value
Returns
AjBool:ajTrue on success

Description

Special processing for known internal (EMBL) tags

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableNew

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

Synopsis

Prototype
AjPFeattable ajFeattableNew (
      const AjPStr name 
);

TypeNameRead/WriteDescription
const AjPStrnameInputName for new feature table (or NULL for unnamed)
AjPFeattable RETURNPointer 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableSetDefname

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

Synopsis

Prototype
void ajFeattableSetDefname (
      AjPFeattable thys,
      const AjPStr setname
);

TypeNameRead/WriteDescription
AjPFeattablethysOutputFeature table
const AjPStrsetnameInputName set by caller
void RETURN

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
ajuintlenInputLength
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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableSetNuc

Sets the type of a feature table as nucleotide

Synopsis

Prototype
void ajFeattableSetNuc (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableSetProt

Sets the type of a feature table as Protein

Synopsis

Prototype
void ajFeattableSetProt (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableSetRange

Set the begin and end range for a feature table

Synopsis

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
ajintfbeginInputBegin position
ajintfendInputEnd 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableReverse

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

Synopsis

Prototype
void ajFeattableReverse (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatReverse

Reverse one feature by reversing all positions and strand.

Synopsis

Prototype
void ajFeatReverse (
      AjPFeature thys,
      ajint ilen
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature object
ajintilenInputSequence 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableNewDna

Constructor for a new DNA feature table

Synopsis

Prototype
AjPFeattable ajFeattableNewDna (
      const AjPStr name
);

TypeNameRead/WriteDescription
const AjPStrnameInputName for new feature table (or NULL for unnamed)
AjPFeattable RETURNPointer 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object to provide the name and type
AjPFeattable RETURNPointer 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableNewProt

Constructor for a new protein feature table

Synopsis

Prototype
AjPFeattable ajFeattableNewProt (
      const AjPStr name
);

TypeNameRead/WriteDescription
const AjPStrnameInputName for new feature table (or NULL for unnamed)
AjPFeattable RETURNPointer 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGfftagAddC

Constructor for a feature GFF3 tag-value pair

Synopsis

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

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const char*tagInputTag name
const AjPStrvalueInputTag value list
ajuint RETURNNumber of values added

Input
tag:(Input)Tag name
value:(Input)Tag value list
Input & Output
thys:(Modify)Feature
Returns
ajuint:Number of values added

Description

Constructor for a feature GFF3 tag-value pair

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGfftagAdd

Constructor for a feature GFF3 tag-value pair

Synopsis

Prototype
ajuint ajFeatGfftagAdd (
      AjPFeature thys,
      const AjPStr tag,
      const AjPStr value
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrtagInputTag name
const AjPStrvalueInputTag value list
ajuint RETURNNumber of values added

Input
tag:(Input)Tag name
value:(Input)Tag value list
Input & Output
thys:(Modify)Feature
Returns
ajuint:Number of values added

Description

Constructor for a feature GFF3 tag-value pair

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableNewFtable

Makes a copy of a feature table.

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

Synopsis

Prototype
AjPFeattable ajFeattableNewFtable (
      const AjPFeattable orig
);

TypeNameRead/WriteDescription
const AjPFeattableorigInputOriginal feature table
AjPFeattable RETURNFeature 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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableNewFtableLimit

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 ajFeattableNewFtableLimit (
      const AjPFeattable orig,
      ajint limit
);

TypeNameRead/WriteDescription
const AjPFeattableorigInputOriginal feature table
ajintlimitInputLimit to number of features copied
AjPFeattable RETURNFeature table copy of the original

Input
orig:(Input)Original feature table
limit:(Input)Limit to number of features copied
Returns
AjPFeattable:Feature table copy of the original

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatNewFeat

Makes a copy of a feature.

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

Synopsis

Prototype
AjPFeature ajFeatNewFeat (
      const AjPFeature orig
);

TypeNameRead/WriteDescription
const AjPFeatureorigInputOriginal feature
AjPFeature RETURNFeature copy of the original

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTrace

Traces (to the debug file) a feature object

Synopsis

Prototype
void ajFeatTrace (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
void RETURN

Input
thys:(Input)Feature
Returns
void:No return value

Description

Traces (to the debug file) a feature object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTagTrace

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

Synopsis

Prototype
void ajFeatTagTrace (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
void RETURN

Input
thys:(Input)Feature
Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGfftagsNew

Creates a structure holding GFF tag value pairs

Synopsis

Prototype
AjPFeatGfftags ajFeatGfftagsNew (
      void
);

TypeNameRead/WriteDescription
AjPFeatGfftags RETURNGFF tag-values structure

Returns
AjPFeatGfftags:GFF tag-values structure

Description

Creates a structure holding GFF tag value pairs

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGfftagsDel

Destroys a structure holding GFF tag value pairs

Synopsis

Prototype
void ajFeatGfftagsDel (
      AjPFeatGfftags* Pthys
);

TypeNameRead/WriteDescription
AjPFeatGfftags*PthysDeleteGFF tag-values structure
void RETURN

Output
Pthys:(Delete)GFF tag-values structure
Returns
void:No return value

Description

Destroys a structure holding GFF tag value pairs

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetGfftags

Returns an object with all feature GFF tag-value pairs

Synopsis

Prototype
AjPFeatGfftags ajFeatGetGfftags (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjPFeatGfftags RETURNGff tags object

Input
thys:(Input)Feature
Returns
AjPFeatGfftags:Gff tags object

Description

Returns an object with all feature GFF tag-value pairs

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatGetParent

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

Synopsis

Prototype
const AjPStr ajFeatGetParent (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
const AjPStr RETURNParent tag

Input
thys:(Input)Feature
Returns
const AjPStr:Parent tag

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTagIter

Returns an iterator over all feature tag-value pairs

Synopsis

Prototype
AjIList ajFeatTagIter (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjIList RETURNList iterator

Input
thys:(Input)Feature
Returns
AjIList:List iterator

Description

Returns an iterator over all feature tag-value pairs

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatSubIter

Returns an iterator over all subfeaturers

Synopsis

Prototype
AjIList ajFeatSubIter (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjIList RETURNList iterator

Input
thys:(Input)Feature
Returns
AjIList:List iterator

Description

Returns an iterator over all subfeaturers

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTagval

Returns the tag-value pairs of a feature object

Synopsis

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

TypeNameRead/WriteDescription
AjIListiterModifyList iterator from ajFeatTagIter
AjPStr*PtagnamOutputTag name
AjPStr*PtagvalOutputTag val
AjBool RETURNajTrue if another tag-value pair was returned

Output
Ptagnam:(Output)Tag name
Ptagval:(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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableTrace

Traces (to the debug file) a complete feature table

Synopsis

Prototype
void ajFeattableTrace (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
void RETURN

Input
thys:(Input)Feature table
Returns
void:No return value

Description

Traces (to the debug file) a complete feature table

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeNuc

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

Synopsis

Prototype
const AjPStr ajFeatTypeNuc (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeProt

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

Synopsis

Prototype
const AjPStr ajFeatTypeProt (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetExternal

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPTabletableInputFeature table
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
table:(Input)Feature table
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetInternal

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

Synopsis

Prototype
const AjPStr ajFeattypeGetInternal (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetInternalEmbl

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

Synopsis

Prototype
const AjPStr ajFeattypeGetInternalEmbl (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetInternalNuc

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

Synopsis

Prototype
const AjPStr ajFeattypeGetInternalNuc (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetInternalPir

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

Synopsis

Prototype
const AjPStr ajFeattypeGetInternalPir (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetInternalProt

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

Synopsis

Prototype
const AjPStr ajFeattypeGetInternalProt (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattypeGetInternalRefseqp

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

Synopsis

Prototype
const AjPStr ajFeattypeGetInternalRefseqp (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

Input
type:(Input)Type name
Returns
const AjPStr:Valid feature type

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagGetNameC

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

Synopsis

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

TypeNameRead/WriteDescription
const char*tagInputType name
const AjPTabletableInputFeature table
AjBool*knowntagOutputajTrue if the tag name is known ajFalse if the default name was substituted
const AjPStr RETURNValid feature tag name

Input
tag:(Input)Type name
table:(Input)Feature table
Output
knowntag:(Output)ajTrue if the tag name is known ajFalse if the default name was substituted
Returns
const AjPStr:Valid feature tag name

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagGetNameS

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrtagInputType name
const AjPTabletableInputFeature table
AjBool*knowntagOutputajTrue if the tag was found in the list of known tags
const AjPStr RETURNValid feature tag name

Input
tag:(Input)Type name
table:(Input)Feature table
Output
knowntag:(Output)ajTrue if the tag was found in the list of known tags
Returns
const AjPStr:Valid feature tag name

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagFormat

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrnameInputTag name
const AjPTabletableInputTag table
AjPStr*retstrOutputstring with formatted value.
void RETURN

Input
name:(Input)Tag name
table:(Input)Tag table
Output
retstr:(Output)string with formatted value.
Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagGetLimit

Returns the controlled vocabulary list for a limited value.

Synopsis

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

TypeNameRead/WriteDescription
const AjPStrnameInputTag name
const AjPTabletableInputTag table
AjPStr*retstrOutputstring with formatted value.
void RETURN

Input
name:(Input)Tag name
table:(Input)Tag table
Output
retstr:(Output)string with formatted value.
Returns
void:No return value

Description

Returns the controlled vocabulary list for a limited value.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatUnused

Dummy function to prevent compiler warnings

Synopsis

Prototype
void ajFeatUnused (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Dummy function to prevent compiler warnings

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeIsCds

Tests whether the feature is a CDS feature

Synopsis

Prototype
AjBool ajFeatTypeIsCds (
      const AjPFeature gf
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNajTrue on success

Input
gf:(Input)Feature
Returns
AjBool:ajTrue on success

Description

Tests whether the feature is a CDS feature

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeMatchC

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
const char*txtInputFeature type name to test
AjBool RETURNajTrue on success

Input
gf:(Input)Feature
txt:(Input)Feature type name to test
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeMatchS

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

Synopsis

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

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
const AjPStrstrInputFeature type name to test
AjBool RETURNajTrue on success

Input
gf:(Input)Feature
str:(Input)Feature type name to test
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatTypeMatchWildS

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

Synopsis

Prototype
AjBool ajFeatTypeMatchWildS (
      const AjPFeature gf,
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
const AjPStrstrInputFeature type name to test
AjBool RETURNajTrue on success

Input
gf:(Input)Feature
str:(Input)Feature type name to test
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNajTrue on success

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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,
      ajuint start,
      ajuint end
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
ajuintstartInputstart of range
ajuintendInputend of range
AjBool RETURNajTrue on success

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.)

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNReturns AJTRUE if it is a child, AJFALSE if it is not a child

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatIsMultiple

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

Synopsis

Prototype
AjBool ajFeatIsMultiple (
      const AjPFeature gf
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNReturns AJTRUE if it is a member

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatIsCompMult

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

Synopsis

Prototype
AjBool ajFeatIsCompMult (
      const AjPFeature gf
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNReturns AJTRUE if it is a complemented multiple

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.)

See Also

See other functions in this section

Availability

In release 6.4.0

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
ajuint ajFeattablePos (
      const AjPFeattable thys,
      ajint ipos
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputTarget feature table.
ajintiposInputPosition.
ajuint RETURNstring position between 1 and length.

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

See Also

See other functions in this section

Availability

In release 6.4.0

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

TypeNameRead/WriteDescription
const AjPFeattablethysInputTarget feature table.
ajuintiminInputStart position.
ajintiposInputPosition.
ajuint RETURNstring position between 1 and length.

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

See Also

See other functions in this section

Availability

In release 6.4.0

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

TypeNameRead/WriteDescription
ajuintilenInputmaximum length.
ajuintiminInputStart position.
ajintiposInputPosition.
ajuint RETURNstring position between 1 and length.

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

See Also

See other functions in this section

Availability

In release 6.4.0

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,
      ajuint ioffset,
      ajuint ilen
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyTarget feature table.
ajuintioffsetInputOffset from start of sequence
ajuintilenInputLength of sequence
AjBool RETURNAjTrue returned if successful.

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).

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattableTrim

Trim a feature table using the Begin and Ends.

Synopsis

Prototype
AjBool ajFeattableTrim (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyTarget feature table.
AjBool RETURNAjTrue returned if successful.

Input & Output
thys:(Modify)Target feature table.
Returns
AjBool:AjTrue returned if successful.

Description

Trim a feature table using the Begin and Ends.

See Also

See other functions in this section

Availability

In release 6.4.0

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)

Synopsis

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

TypeNameRead/WriteDescription
AjPFeatureftModifyTarget feature
ajuintioffsetInputOffset from start of sequence
ajuintbeginInputRange start of sequence
ajuintendInputRange end of sequence
AjBooldobeginInputReset begin
AjBooldoendInputReset end
AjBool RETURNAjTrue returned if successful.

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)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeattagIsNote

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

Synopsis

Prototype
AjBool ajFeattagIsNote (
      const AjPStr tag
);

TypeNameRead/WriteDescription
const AjPStrtagInputFeature tag
AjBool RETURNajTrue on success

Input
tag:(Input)Feature tag
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatExit

Cleans up feature table internal memory

Synopsis

Prototype
void ajFeatExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up feature table internal memory

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajFeatWarn

Formatted write as a warning message.

Synopsis

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

TypeNameRead/WriteDescription
const char*fmtInputFormat string
...varargVarargFormat arguments.
void RETURN

Input
fmt:(Input)Format string
:(Vararg)Format arguments.
Returns
void:No return value

Description

Formatted write as a warning message.

See Also

See other functions in this section

Availability

In release 6.4.0