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:
ajFeatNewConstructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewSubConstructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewIISimple constructor with only start and end positions
ajFeatNewIISubSimple constructor with only start and end positions
ajFeatNewIIRevSimple constructor with only start and end positions, sets feature to be on the reverse strand
ajFeatNewIIRevSubSimple constructor with only start and end positions, sets feature to be on the reverse strand
ajFeatNewProtConstructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewProtSubConstructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewProtFlagsConstructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatNewProtFlagsSubConstructor - must specify associated 'ajFeattable' to which the new feature is automatically added!
ajFeatCompByStartCompare two features by their start.
ajFeatCompByEndCompare two features by their end.
ajFeatCompByGroupCompare two features by their group and exon numbers
ajFeatCompByTypeCompare two features by their type (key).
ajFeatNewNucConstructor for a new feature, automatically added to the specified table.
ajFeatNewNucSubConstructor for a new feature, automatically added to the specified table.
ajFeatNewNucFlagsConstructor for a new feature, automatically added to the specified table.
ajFeatNewNucFlagsSubConstructor for a new feature, automatically added to the specified table.


Function ajFeatNew

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

Prototype

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

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

From EMBOSS 2.0.0


Function ajFeatNewSub

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewII

Simple constructor with only start and end positions

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

From EMBOSS 2.1.0


Function ajFeatNewIISub

Simple constructor with only start and end positions

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewIIRev

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

Prototype

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

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

From EMBOSS 2.8.0


Function ajFeatNewIIRevSub

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewProt

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

Prototype

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

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

From EMBOSS 2.0.0


Function ajFeatNewProtSub

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewProtFlags

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewProtFlagsSub

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatCompByStart

Compare two features by their start.

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.

From EMBOSS 6.4.0


Function ajFeatCompByEnd

Compare two features by their end.

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.

From EMBOSS 6.4.0


Function ajFeatCompByGroup

Compare two features by their group and exon numbers

Prototype

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

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.

From EMBOSS 6.4.0


Function ajFeatCompByType

Compare two features by their type (key).

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.

From EMBOSS 6.4.0


Function ajFeatNewNuc

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewNucSub

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewNucFlags

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatNewNucFlagsSub

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

Prototype

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

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

From EMBOSS 6.4.0


Section: Feature Object Destructors

(Simple minded) object destruction by release of memory.

No reference counting (for now).

Functions:
ajFeattableDelDestructor for ajFeattable objects. If the given object (pointer) is NULL, or a NULL pointer, simply returns.
ajFeatDelDestructor for AjPFeature objects. If the given object (pointer) is NULL, or a NULL pointer, simply returns.


Function ajFeattableDel

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

Prototype

void ajFeattableDel (
      AjPFeattable* pthis
);

TypeNameRead/WriteDescription
AjPFeattable*pthisDeletePointer to the object to be deleted. The pointer is always deleted.
void RETURN

From EMBOSS 2.1.0


Function ajFeatDel

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

Prototype

void ajFeatDel (
      AjPFeature* pthis
);

TypeNameRead/WriteDescription
AjPFeature*pthisDeletePointer to the object to be deleted. The pointer is always deleted.
void RETURN

From EMBOSS 1.0.0


Section: Feature Assignments

Functions:
ajFeatSortByTypeSort Feature table by Type.
ajFeatSortByStartSort Feature table by Start position.
ajFeatSortByEndSort Feature table by End position.


Function ajFeatSortByType

Sort Feature table by Type.

Prototype

void ajFeatSortByType (
      AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattableFeattabModifyFeature table to be sorted.
void RETURN

From EMBOSS 1.0.0


Function ajFeatSortByStart

Sort Feature table by Start position.

Prototype

void ajFeatSortByStart (
      AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattableFeattabModifyFeature table to be sorted.
void RETURN

From EMBOSS 1.0.0


Function ajFeatSortByEnd

Sort Feature table by End position.

Prototype

void ajFeatSortByEnd (
      AjPFeattable Feattab
);

TypeNameRead/WriteDescription
AjPFeattableFeattabModifyFeature table to be sorted.
void RETURN

From EMBOSS 1.0.0


Section: Feature Table Modifiers

Functions:
ajFeattableAddMethod to add a new AjPFeature to a AjPFeattable


Function ajFeattableAdd

Method to add a new AjPFeature to a AjPFeattable

Prototype

void ajFeattableAdd (
      AjPFeattable thys,
      AjPFeature feature
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyThe feature table
AjPFeaturefeatureModifyFeature to be added to the set
void RETURN

From EMBOSS 2.1.0


Section: Feature Object Operators

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

Functions:
ajFeattableClearClears a feature table of all features
ajFeatTypeGetCategoryreturns the category name for a feature type
ajFeattableGetEntryReturn the full text
ajFeattableGetQryCReturns 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.
ajFeattableGetQrySReturns 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.
ajFeattableGetTypeCReturns 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.
ajFeattableGetTypeSReturns 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.
ajFeattableGetXrefsReturns all cross-references from a feature table
ajFeatframeGetFrameConverts a frame number in the range 0 to 3 to a GFF frame character or '.' as the general default
ajFeatframeGetFrameNucConverts a frame number in the range 0 to 3 to a GFF frame character or '0' for the nucleotide default
ajFeatstrandGetStrandConverts a strand number to a GFF strand character. NULL characters are converted to '+' All other values are simply cast to character.
ajFeattableIsNucReturns ajTrue if a feature table is nucleotide
ajFeattableIsProtReturns ajTrue if a feature table is protein
ajFeattableGetBeginReturns the feature table start position, or 1 if no start has been set.
ajFeattableGetEndReturns the features table end position, or the feature table length if no end has been set.
ajFeattableGetLenReturns the sequence length of a feature table
ajFeattableGetNameReturns 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.
ajFeattableGetSizeReturns the size of a feature table object.
ajFeatGetFlagsReturns 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.
ajFeatGetSeqReturns the sequence matching a feature.
ajFeatGetSeqJoinReturns 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.
ajFeatGetRemoteseqReturns a sequence entry from a feature location which points to another entry
ajFeatGetXrefsReturns all cross-references from a feature
ajFeatLocMarkReturns a sequence entry converted to lower case where a feature location matches.
ajFeatGetNoteCFinds a named note tag (with a * prefix)
ajFeatGetNoteCIFinds a named note tag (with a * prefix)
ajFeatGetNoteSIFinds a named note tag (with a * prefix)
ajFeatGetNoteSFinds a named note tag (with a * prefix)
ajFeatGetTagCReturns the nth value of a named feature tag.
ajFeatGetTagSReturns the nth value of a named feature tag.
ajFeatGetTypeReturns 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.
ajFeatGetSourceReturns the source name of a feature object.
ajFeatGetStartReturns the start position of a feature object.
ajFeatGetStrandReturns the strand of a feature object.
ajFeatGetEndReturns the end position of a feature object.
ajFeatGetLengthReturns the sequence length of a feature object.
ajFeatGetScoreReturns the score of a feature object.
ajFeatGetForwardReturns the direction of a feature object.
ajFeatGetFrameReturns the reading frame of a feature object.
ajFeatGetTranslationReturns translation tag value
ajFeatTestTemporary testing function for feature handling to be deleted when all is working happily
ajFeatVocabGetTagsReturns tags table for a named feature format
ajFeatVocabGetTagsNucReturns tags table for a named nucleotide feature format
ajFeatVocabGetTagsProtReturns tags table for a named protein feature format
ajFeatVocabGetTypesReturns types table for a named feature format
ajFeatVocabGetTypesNucReturns types table for a named nucleotide feature format
ajFeatVocabGetTypesProtReturns types table for a named protein feature format
ajFeatVocabInitInitialises feature table internals for a named feature format
ajFeatVocabInitNucInitialises feature table internals for a named feature format
ajFeatVocabInitProtInitialises feature table internals for a named feature format
ajFeatSetDescAppSets the description for a feature
ajFeatSetDescSets the description for a feature
ajFeatSetSourceSets the source for a feature
ajFeatSetScoreSets the score for a feature
ajFeatSetStrandSets the strand for a feature
ajFeatTagSetCSets a feature tag value
ajFeatTagSetSets a feature tag value
ajFeattagSpecialGff2Special processing for known GFF tags
ajFeattagSpecialGff3Special processing for known GFF3 tags
ajFeatTagAddCCSets a feature tag value, creating a new feature tag even if one already exists.
ajFeatTagAddCSets a feature tag value, creating a new feature tag even if one already exists.
ajFeatTagAddSets a feature tag value, creating a new feature tag even if one already exists.
ajFeattagSpecialSpecial processing for known internal (EMBL) tags
ajFeattableNewConstructor for a new (generic) feature table. Does not define the feature table type.
ajFeattableSetDefnameProvides a unique (for this program run) name for a feature table.
ajFeattableSetLengthSets the length of a feature table with the length of the source sequence.
ajFeattableSetNucSets the type of a feature table as nucleotide
ajFeattableSetProtSets the type of a feature table as Protein
ajFeattableSetRangeSet the begin and end range for a feature table
ajFeattableReverseReverse the features in a feature table by iterating through and reversing all positions and strands.
ajFeatReverseReverse one feature by reversing all positions and strand.
ajFeattableNewDnaConstructor for a new DNA feature table
ajFeattableNewSeqConstructor for a new feature table for an existing sequence. The feature table type is determined by the sequence type.
ajFeattableNewProtConstructor for a new protein feature table
ajFeatGfftagAddCConstructor for a feature GFF3 tag-value pair
ajFeatGfftagAddConstructor for a feature GFF3 tag-value pair
ajFeattableNewFtableMakes a copy of a feature table.
ajFeattableNewFtableLimitMakes a copy of a feature table using only a limited number of features.
ajFeatNewFeatMakes a copy of a feature.
ajFeatTraceTraces (to the debug file) a feature object
ajFeatTagTraceTraces (to the debug file) the tag-value pairs of a feature object
ajFeatGfftagsNewCreates a structure holding GFF tag value pairs
ajFeatGfftagsDelDestroys a structure holding GFF tag value pairs
ajFeatGetGfftagsReturns an object with all feature GFF tag-value pairs
ajFeatGetParentReturns the GFF Parent tag of a feature with GFF tag-value pairs
ajFeatTagIterReturns an iterator over all feature tag-value pairs
ajFeatSubIterReturns an iterator over all subfeaturers
ajFeatTagvalReturns the tag-value pairs of a feature object
ajFeattableTraceTraces (to the debug file) a complete feature table
ajFeatTypeNucGiven a feature type name, returns the valid feature type for the internal DNA feature table
ajFeatTypeProtGiven a feature type name, returns the valid feature type for the internal protein feature table
ajFeattypeGetExternalGiven a feature type name, returns the valid feature type for a feature table
ajFeattypeGetInternalGiven a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalEmblGiven a feature type name, returns the valid feature type for an EMBL format feature table
ajFeattypeGetInternalNucGiven a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalPirGiven a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalProtGiven a feature type name, returns the valid feature type for an internal feature table
ajFeattypeGetInternalRefseqpGiven a feature type name, returns the valid feature type for a REFSEQP format feature table
ajFeattagGetNameCGiven a feature tag name, returns the valid feature tag name for a feature table
ajFeattagGetNameSGiven a feature tag name, returns the valid feature tag name for a feature table
ajFeattagFormatConverts a feature tag value into the correct format, after checking it is an acceptable value
ajFeattagGetLimitReturns the controlled vocabulary list for a limited value.
ajFeatUnusedDummy function to prevent compiler warnings
ajFeatTypeIsCdsTests whether the feature is a CDS feature
ajFeatTypeMatchCTests whether the feature type matches a given string including testing for alternative names
ajFeatTypeMatchSTests whether the feature type matches a given string including testing for alternative names
ajFeatTypeMatchWildSTests whether the feature type matches a given wildcard string including testing for alternative names
ajFeatIsLocalTests whether the feature is local to the sequence. Returns AJTRUE if it is local, AJFALSE if remote.
ajFeatIsLocalRangeTests 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.)
ajFeatIsChildTests whether the feature is a child member of a join The parent (first) feature of a join gives: ajFeatIsChild == ajFalse && ajFeatIsMultiple == ajTrue
ajFeatIsMultipleTests whether the feature is a member of a join, group order or one_of
ajFeatIsCompMultTests whether the feature is a member of a complement around a multiple (join, etc.)
ajFeattablePosConverts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.
ajFeattablePosIConverts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.
ajFeattablePosIIConverts a position into a true position. If ipos is negative, it is counted from the end of the sequence rather than the beginning.
ajFeattableTrimOffTrim a feature table using the Begin and Ends.
ajFeattableTrimTrim a feature table using the Begin and Ends.
ajFeatTrimOffRangeTrim a feature table using the Begin and Ends.
ajFeattagIsNoteTests whether the feature tag is a note (the default feature tag)
ajFeatExitCleans up feature table internal memory
ajFeatWarnFormatted write as a warning message.


Function ajFeattableClear

Clears a feature table of all features

Prototype

void ajFeattableClear (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table
void RETURN

From EMBOSS 2.1.0


Function ajFeatTypeGetCategory

returns the category name for a feature type

Prototype

const AjPStr ajFeatTypeGetCategory (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputFeature type
const AjPStr RETURNFeature category

From EMBOSS 6.1.0


Function ajFeattableGetEntry

Return the full text

Prototype

const AjPStr ajFeattableGetEntry (
      const AjPFeattable thys
);

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

From EMBOSS 6.4.0


Function ajFeattableGetQryC

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

Prototype

const char* ajFeattableGetQryC (
      const AjPFeattable ftable
);

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

From EMBOSS 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.

Prototype

const AjPStr ajFeattableGetQryS (
      const AjPFeattable ftable
);

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

From EMBOSS 6.4.0


Function ajFeattableGetTypeC

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

Prototype

const char* ajFeattableGetTypeC (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
const char* RETURNFeature table type.

From EMBOSS 4.0.0


Function ajFeattableGetTypeS

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

Prototype

const AjPStr ajFeattableGetTypeS (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
const AjPStr RETURNFeature table name.

From EMBOSS 4.0.0


Function ajFeattableGetXrefs

Returns all cross-references from a feature table

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatframeGetFrame

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

Prototype

char ajFeatframeGetFrame (
      ajint frame
);

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

From EMBOSS 6.4.0


Function ajFeatframeGetFrameNuc

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

Prototype

char ajFeatframeGetFrameNuc (
      ajint frame
);

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

From EMBOSS 6.4.0


Function ajFeatstrandGetStrand

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

Prototype

char ajFeatstrandGetStrand (
      ajint strand
);

TypeNameRead/WriteDescription
ajintstrandInputStrand
char RETURNGFF character for this strand.

From EMBOSS 6.4.0


Function ajFeattableIsNuc

Returns ajTrue if a feature table is nucleotide

Prototype

AjBool ajFeattableIsNuc (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
AjBool RETURNajTrue for a protein feature table

From EMBOSS 2.5.0


Function ajFeattableIsProt

Returns ajTrue if a feature table is protein

Prototype

AjBool ajFeattableIsProt (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
AjBool RETURNajTrue for a protein feature table

From EMBOSS 2.5.0


Function ajFeattableGetBegin

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

Prototype

ajint ajFeattableGetBegin (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputfeature table object
ajint RETURNStart position.

From EMBOSS 6.2.0


Function ajFeattableGetEnd

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

Prototype

ajint ajFeattableGetEnd (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputfeature table object
ajint RETURNEnd position.

From EMBOSS 6.2.0


Function ajFeattableGetLen

Returns the sequence length of a feature table

Prototype

ajint ajFeattableGetLen (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
ajint RETURNLength in bases or residues

From EMBOSS 6.2.0


Function ajFeattableGetName

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

Prototype

const AjPStr ajFeattableGetName (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
const AjPStr RETURNFeature table name.

From EMBOSS 2.1.0


Function ajFeattableGetSize

Returns the size of a feature table object.

Prototype

ajuint ajFeattableGetSize (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
ajuint RETURNFeature table size.

From EMBOSS 6.1.0


Function ajFeatGetFlags

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

Prototype

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

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

From EMBOSS 6.2.0


Function ajFeatGetSeq

Returns the sequence matching a feature.

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatGetSeqJoin

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

Prototype

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

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

From EMBOSS 6.2.0


Function ajFeatGetRemoteseq

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

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatGetXrefs

Returns all cross-references from a feature

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatLocMark

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

Prototype

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

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

From EMBOSS 4.1.0


Function ajFeatGetNoteC

Finds a named note tag (with a * prefix)

Prototype

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

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

From EMBOSS 4.0.0


Function ajFeatGetNoteCI

Finds a named note tag (with a * prefix)

Prototype

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

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)

From EMBOSS 4.0.0


Function ajFeatGetNoteSI

Finds a named note tag (with a * prefix)

Prototype

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

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)

From EMBOSS 6.2.0


Function ajFeatGetNoteS

Finds a named note tag (with a * prefix)

Prototype

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

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

From EMBOSS 6.2.0


Function ajFeatGetTagC

Returns the nth value of a named feature tag.

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatGetTagS

Returns the nth value of a named feature tag.

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatGetType

Returns the type (key) of a feature object. This is a copy of the pointer to the type, and is still owned by the feature and is not to be destroyed.

Prototype

const AjPStr ajFeatGetType (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStr RETURNFeature type, read only

From EMBOSS 2.1.0


Function ajFeatGetSource

Returns the source name of a feature object.

Prototype

const AjPStr ajFeatGetSource (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
const AjPStr RETURNFeature source name

From EMBOSS 4.0.0


Function ajFeatGetStart

Returns the start position of a feature object.

Prototype

ajuint ajFeatGetStart (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajuint RETURNFeature start position

From EMBOSS 2.1.0


Function ajFeatGetStrand

Returns the strand of a feature object.

Prototype

char ajFeatGetStrand (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
char RETURNFeature strand code

From EMBOSS 4.0.0


Function ajFeatGetEnd

Returns the end position of a feature object.

Prototype

ajuint ajFeatGetEnd (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajuint RETURNFeature end position

From EMBOSS 2.1.0


Function ajFeatGetLength

Returns the sequence length of a feature object.

Prototype

ajuint ajFeatGetLength (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajuint RETURNFeature length

From EMBOSS 4.0.0


Function ajFeatGetScore

Returns the score of a feature object.

Prototype

float ajFeatGetScore (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
float RETURNFeature score

From EMBOSS 4.0.0


Function ajFeatGetForward

Returns the direction of a feature object.

Prototype

AjBool ajFeatGetForward (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
AjBool RETURNajTrue for a forward direction, ajFalse for reverse

From EMBOSS 2.1.0


Function ajFeatGetFrame

Returns the reading frame of a feature object.

Prototype

ajint ajFeatGetFrame (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature object
ajint RETURNFeature reading frame (zero for undefined)

From EMBOSS 2.1.0


Function ajFeatGetTranslation

Returns translation tag value

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatTest

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

Prototype

void ajFeatTest (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 2.0.0


Function ajFeatVocabGetTags

Returns tags table for a named feature format

Prototype

const AjPTable ajFeatVocabGetTags (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabGetTagsNuc

Returns tags table for a named nucleotide feature format

Prototype

const AjPTable ajFeatVocabGetTagsNuc (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabGetTagsProt

Returns tags table for a named protein feature format

Prototype

const AjPTable ajFeatVocabGetTagsProt (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabGetTypes

Returns types table for a named feature format

Prototype

const AjPTable ajFeatVocabGetTypes (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabGetTypesNuc

Returns types table for a named nucleotide feature format

Prototype

const AjPTable ajFeatVocabGetTypesNuc (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabGetTypesProt

Returns types table for a named protein feature format

Prototype

const AjPTable ajFeatVocabGetTypesProt (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabInit

Initialises feature table internals for a named feature format

Prototype

const AjPTable ajFeatVocabInit (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabInitNuc

Initialises feature table internals for a named feature format

Prototype

const AjPTable ajFeatVocabInitNuc (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatVocabInitProt

Initialises feature table internals for a named feature format

Prototype

const AjPTable ajFeatVocabInitProt (
      const char* name
);

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

From EMBOSS 6.4.0


Function ajFeatSetDescApp

Sets the description for a feature

Prototype

void ajFeatSetDescApp (
      AjPFeature thys,
      const AjPStr desc
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrdescInputFeature description (simple text)
void RETURN

From EMBOSS 2.3.0


Function ajFeatSetDesc

Sets the description for a feature

Prototype

void ajFeatSetDesc (
      AjPFeature thys,
      const AjPStr desc
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrdescInputFeature description (simple text)
void RETURN

From EMBOSS 2.0.0


Function ajFeatSetSource

Sets the source for a feature

Prototype

void ajFeatSetSource (
      AjPFeature thys,
      const AjPStr source
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
const AjPStrsourceInputFeature source
void RETURN

From EMBOSS 6.4.0


Function ajFeatSetScore

Sets the score for a feature

Prototype

void ajFeatSetScore (
      AjPFeature thys,
      float score
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
floatscoreInputScore value
void RETURN

From EMBOSS 4.0.0


Function ajFeatSetStrand

Sets the strand for a feature

Prototype

void ajFeatSetStrand (
      AjPFeature thys,
      AjBool rev
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature
AjBoolrevInputTrue if reverse strand
void RETURN

From EMBOSS 4.0.0


Function ajFeatTagSetC

Sets a feature tag value

Prototype

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

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

From EMBOSS 2.0.0


Function ajFeatTagSet

Sets a feature tag value

Prototype

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

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

From EMBOSS 2.0.0


Function ajFeattagSpecialGff2

Special processing for known GFF tags

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattagSpecialGff3

Special processing for known GFF3 tags

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatTagAddCC

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

Prototype

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

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"

From EMBOSS 2.4.0


Function ajFeatTagAddC

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

Prototype

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

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"

From EMBOSS 2.4.0


Function ajFeatTagAdd

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

Prototype

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

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

From EMBOSS 2.0.0


Function ajFeattagSpecial

Special processing for known internal (EMBL) tags

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattableNew

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

Prototype

AjPFeattable ajFeattableNew (
      const AjPStr name 
);

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

From EMBOSS 2.0.0


Function ajFeattableSetDefname

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

Prototype

void ajFeattableSetDefname (
      AjPFeattable thys,
      const AjPStr setname
);

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

From EMBOSS 6.2.0


Function ajFeattableSetLength

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

Prototype

void ajFeattableSetLength (
      AjPFeattable thys,
      ajuint len
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
ajuintlenInputLength
void RETURN

From EMBOSS 6.0.0


Function ajFeattableSetNuc

Sets the type of a feature table as nucleotide

Prototype

void ajFeattableSetNuc (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
void RETURN

From EMBOSS 4.0.0


Function ajFeattableSetProt

Sets the type of a feature table as Protein

Prototype

void ajFeattableSetProt (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
void RETURN

From EMBOSS 2.1.0


Function ajFeattableSetRange

Set the begin and end range for a feature table

Prototype

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

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
ajintfbeginInputBegin position
ajintfendInputEnd position
void RETURN

From EMBOSS 2.5.0


Function ajFeattableReverse

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

Prototype

void ajFeattableReverse (
      AjPFeattable thys
);

TypeNameRead/WriteDescription
AjPFeattablethysModifyFeature table object
void RETURN

From EMBOSS 2.5.0


Function ajFeatReverse

Reverse one feature by reversing all positions and strand.

Prototype

void ajFeatReverse (
      AjPFeature thys,
      ajint ilen
);

TypeNameRead/WriteDescription
AjPFeaturethysModifyFeature object
ajintilenInputSequence length
void RETURN

From EMBOSS 2.5.0


Function ajFeattableNewDna

Constructor for a new DNA feature table

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

From EMBOSS 2.0.0


Function ajFeattableNewSeq

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

Prototype

AjPFeattable ajFeattableNewSeq (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object to provide the name and type
AjPFeattable RETURNPointer to a new (empty) feature table

From EMBOSS 2.0.0


Function ajFeattableNewProt

Constructor for a new protein feature table

Prototype

AjPFeattable ajFeattableNewProt (
      const AjPStr name
);

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

From EMBOSS 2.0.0


Function ajFeatGfftagAddC

Constructor for a feature GFF3 tag-value pair

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatGfftagAdd

Constructor for a feature GFF3 tag-value pair

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattableNewFtable

Makes a copy of a feature table.

Prototype

AjPFeattable ajFeattableNewFtable (
      const AjPFeattable orig
);

TypeNameRead/WriteDescription
const AjPFeattableorigInputOriginal feature table
AjPFeattable RETURNFeature table copy of the original

From EMBOSS 6.2.0


Function ajFeattableNewFtableLimit

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

Prototype

AjPFeattable ajFeattableNewFtableLimit (
      const AjPFeattable orig,
      ajint limit
);

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

From EMBOSS 6.2.0


Function ajFeatNewFeat

Makes a copy of a feature.

Prototype

AjPFeature ajFeatNewFeat (
      const AjPFeature orig
);

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

From EMBOSS 6.2.0


Function ajFeatTrace

Traces (to the debug file) a feature object

Prototype

void ajFeatTrace (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
void RETURN

From EMBOSS 1.0.0


Function ajFeatTagTrace

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

Prototype

void ajFeatTagTrace (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
void RETURN

From EMBOSS 2.0.0


Function ajFeatGfftagsNew

Creates a structure holding GFF tag value pairs

Prototype

AjPFeatGfftags ajFeatGfftagsNew (
      void
);

TypeNameRead/WriteDescription
AjPFeatGfftags RETURNGFF tag-values structure

From EMBOSS 6.4.0


Function ajFeatGfftagsDel

Destroys a structure holding GFF tag value pairs

Prototype

void ajFeatGfftagsDel (
      AjPFeatGfftags* Pthys
);

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

From EMBOSS 6.4.0


Function ajFeatGetGfftags

Returns an object with all feature GFF tag-value pairs

Prototype

AjPFeatGfftags ajFeatGetGfftags (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjPFeatGfftags RETURNGff tags object

From EMBOSS 6.4.0


Function ajFeatGetParent

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

Prototype

const AjPStr ajFeatGetParent (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
const AjPStr RETURNParent tag

From EMBOSS 6.4.0


Function ajFeatTagIter

Returns an iterator over all feature tag-value pairs

Prototype

AjIList ajFeatTagIter (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjIList RETURNList iterator

From EMBOSS 2.0.0


Function ajFeatSubIter

Returns an iterator over all subfeaturers

Prototype

AjIList ajFeatSubIter (
      const AjPFeature thys
);

TypeNameRead/WriteDescription
const AjPFeaturethysInputFeature
AjIList RETURNList iterator

From EMBOSS 6.4.0


Function ajFeatTagval

Returns the tag-value pairs of a feature object

Prototype

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

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

From EMBOSS 2.0.0


Function ajFeattableTrace

Traces (to the debug file) a complete feature table

Prototype

void ajFeattableTrace (
      const AjPFeattable thys
);

TypeNameRead/WriteDescription
const AjPFeattablethysInputFeature table
void RETURN

From EMBOSS 2.0.0


Function ajFeatTypeNuc

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

Prototype

const AjPStr ajFeatTypeNuc (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.0.0


Function ajFeatTypeProt

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

Prototype

const AjPStr ajFeatTypeProt (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.0.0


Function ajFeattypeGetExternal

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattypeGetInternal

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

Prototype

const AjPStr ajFeattypeGetInternal (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.4.0


Function ajFeattypeGetInternalEmbl

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

Prototype

const AjPStr ajFeattypeGetInternalEmbl (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.4.0


Function ajFeattypeGetInternalNuc

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

Prototype

const AjPStr ajFeattypeGetInternalNuc (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.4.0


Function ajFeattypeGetInternalPir

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

Prototype

const AjPStr ajFeattypeGetInternalPir (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.4.0


Function ajFeattypeGetInternalProt

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

Prototype

const AjPStr ajFeattypeGetInternalProt (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.4.0


Function ajFeattypeGetInternalRefseqp

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

Prototype

const AjPStr ajFeattypeGetInternalRefseqp (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputType name
const AjPStr RETURNValid feature type

From EMBOSS 6.4.0


Function ajFeattagGetNameC

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattagGetNameS

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattagFormat

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

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeattagGetLimit

Returns the controlled vocabulary list for a limited value.

Prototype

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

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

From EMBOSS 6.4.0


Function ajFeatUnused

Dummy function to prevent compiler warnings

Prototype

void ajFeatUnused (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 1.0.0


Function ajFeatTypeIsCds

Tests whether the feature is a CDS feature

Prototype

AjBool ajFeatTypeIsCds (
      const AjPFeature gf
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNajTrue on success

From EMBOSS 6.0.0


Function ajFeatTypeMatchC

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

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatTypeMatchS

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

Prototype

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

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

From EMBOSS 6.1.0


Function ajFeatTypeMatchWildS

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

Prototype

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

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

From EMBOSS 6.2.0


Function ajFeatIsLocal

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

Prototype

AjBool ajFeatIsLocal (
      const AjPFeature gf
);

TypeNameRead/WriteDescription
const AjPFeaturegfInputFeature
AjBool RETURNajTrue on success

From EMBOSS 2.1.0


Function ajFeatIsLocalRange

Tests whether the feature is local and in the specified range of the sequence. Returns AJTRUE if it is local and within the range. (Any label location is assumed to be outside the range.)

Prototype

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

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

From EMBOSS 2.1.0


Function ajFeatIsChild

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

Prototype

AjBool ajFeatIsChild (
      const AjPFeature gf
);

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

From EMBOSS 2.5.0


Function ajFeatIsMultiple

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

Prototype

AjBool ajFeatIsMultiple (
      const AjPFeature gf
);

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

From EMBOSS 2.5.0


Function ajFeatIsCompMult

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

Prototype

AjBool ajFeatIsCompMult (
      const AjPFeature gf
);

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

From EMBOSS 2.5.0


Function ajFeattablePos

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

Prototype

ajuint ajFeattablePos (
      const AjPFeattable thys,
      ajint ipos
);

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

From EMBOSS 2.5.0


Function ajFeattablePosI

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

Prototype

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

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

From EMBOSS 2.5.0


Function ajFeattablePosII

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

Prototype

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

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

From EMBOSS 2.5.0


Function ajFeattableTrimOff

Trim a feature table using the Begin and Ends.

Prototype

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

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

From EMBOSS 2.7.0


Function ajFeattableTrim

Trim a feature table using the Begin and Ends.

Prototype

AjBool ajFeattableTrim (
      AjPFeattable thys
);

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

From EMBOSS 6.3.0


Function ajFeatTrimOffRange

Trim a feature table using the Begin and Ends.

Prototype

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

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.

From EMBOSS 2.7.0


Function ajFeattagIsNote

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

Prototype

AjBool ajFeattagIsNote (
      const AjPStr tag
);

TypeNameRead/WriteDescription
const AjPStrtagInputFeature tag
AjBool RETURNajTrue on success

From EMBOSS 6.0.0


Function ajFeatExit

Cleans up feature table internal memory

Prototype

void ajFeatExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 2.0.0


Function ajFeatWarn

Formatted write as a warning message.

Prototype

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

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

From EMBOSS 6.4.0