htsjdk.tribble.gff

Interface Gff3Feature

All Superinterfaces:

Feature, Locatable

All Known Implementing Classes:

Gff3FeatureImpl

public interface Gff3Feature
extends Feature

Gff3 format spec is defined at https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Discontinuous features which are split between multiple lines in the gff files are implemented as separate features linked as "co-features"

Method Summary

Modifier and Type	Method and Description
java.util.Set<? extends Gff3Feature>	flatten() Flatten this feature and all descendents into a set of features.
default java.lang.String	getAlias()
java.util.Set<? extends Gff3Feature>	getAncestors() Get set of all features this feature descends from, through chains of Parent attributes.
default java.lang.String	getAttribute(java.lang.String key)
default java.util.Map<java.lang.String,java.lang.String>	getAttributes()
Gff3BaseData	getBaseData() Get BaseData object which contains all the basic information of the feature
java.util.Set<? extends Gff3Feature>	getChildren() Gets set of features for which this feature is a parent
java.util.Set<? extends Gff3Feature>	getCoFeatures() Get set of co-features.
default java.lang.String	getContig() Gets the contig name for the contig this is mapped to.
java.util.Set<? extends Gff3Feature>	getDescendents() Get set of all features descended from this features, through chains of Parent attributes.
default int	getEnd()
default java.lang.String	getID()
default java.lang.String	getName()
java.util.Set<? extends Gff3Feature>	getParents() Gets set of parent features
default int	getPhase()
default java.lang.String	getSource()
default int	getStart()
default Strand	getStrand()
java.util.Set<? extends Gff3Feature>	getTopLevelFeatures() Get the set of top level features from which this feature is descended.
default java.lang.String	getType()
boolean	hasChildren()
boolean	hasCoFeatures()
boolean	hasParents()
boolean	isTopLevelFeature()

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Method Detail

getTopLevelFeatures

java.util.Set<? extends Gff3Feature> getTopLevelFeatures()

Get the set of top level features from which this feature is descended. Top level features are features with no linked parents

Returns:

set of top level feature from which this feature is descended

isTopLevelFeature

boolean isTopLevelFeature()

getSource

default java.lang.String getSource()

getEnd

default int getEnd()

Specified by:

getEnd in interface Locatable

Returns:

1-based closed-ended position, undefined if getContig() == null

getStrand

default Strand getStrand()

getPhase

default int getPhase()

getType

default java.lang.String getType()

getContig

default java.lang.String getContig()

Description copied from interface: Locatable

Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.

Specified by:

getContig in interface Locatable

Returns:

name of the contig this is mapped to, potentially null

getStart

default int getStart()

Specified by:

getStart in interface Locatable

Returns:

1-based start position, undefined if getContig() == null

getAttribute

default java.lang.String getAttribute(java.lang.String key)

getAttributes

default java.util.Map<java.lang.String,java.lang.String> getAttributes()

getID

default java.lang.String getID()

getName

default java.lang.String getName()

getAlias

default java.lang.String getAlias()

getBaseData

Gff3BaseData getBaseData()

Get BaseData object which contains all the basic information of the feature

Returns:

getParents

java.util.Set<? extends Gff3Feature> getParents()

Gets set of parent features

Returns:

set of parent features

getChildren

java.util.Set<? extends Gff3Feature> getChildren()

Gets set of features for which this feature is a parent

Returns:

set of child features

getAncestors

java.util.Set<? extends Gff3Feature> getAncestors()

Get set of all features this feature descends from, through chains of Parent attributes. If Derives_From exists for this feature, then only features along the inheritance path specified by the Derives_From attribute should be included as ancestors of this feature

Returns:

set of ancestor features

getDescendents

java.util.Set<? extends Gff3Feature> getDescendents()

Get set of all features descended from this features, through chains of Parent attributes. If Derives_From attribute exists for a feature, it should only be included as a descendent of this feature if the inheritance path specified by its Derives_From attribute includes this feature

Returns:

set of descendents

getCoFeatures

java.util.Set<? extends Gff3Feature> getCoFeatures()

Get set of co-features. Co-features correspond to the other lines in the gff file that together make up a single discontinuous feature

Returns:

set of co-features

flatten

java.util.Set<? extends Gff3Feature> flatten()

Flatten this feature and all descendents into a set of features. The Derives_From attribute is respected if it exists for this feature

Returns:

set of this feature and all descendents

hasParents

boolean hasParents()

hasChildren

boolean hasChildren()

hasCoFeatures

boolean hasCoFeatures()