htsjdk.tribble.gff

Class Gff3FeatureImpl

java.lang.Object

htsjdk.tribble.gff.Gff3FeatureImpl

All Implemented Interfaces:

Locatable, Feature, Gff3Feature

public class Gff3FeatureImpl
extends java.lang.Object
implements Gff3Feature

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"

Constructor Summary

Constructors

Constructor and Description
Gff3FeatureImpl(Gff3BaseData baseData)
Gff3FeatureImpl(java.lang.String contig, java.lang.String source, java.lang.String type, int start, int end, java.lang.Double score, Strand strand, int phase, java.util.Map<java.lang.String,java.util.List<java.lang.String>> attributes)

Method Summary

Modifier and Type	Method and Description
void	addCoFeature(Gff3FeatureImpl coFeature) Add a feature as a coFeature of this feature.
void	addParent(Gff3FeatureImpl parent)
boolean	equals(java.lang.Object other)
java.util.Set<Gff3FeatureImpl>	flatten() flatten this feature and all descendents into a set of features
java.util.Set<Gff3FeatureImpl>	getAncestors() Get set of all features this feature descends from, through chains of Parent attributes.
Gff3BaseData	getBaseData() Get BaseData object which contains all the basic information of the feature
java.util.Set<Gff3FeatureImpl>	getChildren() Gets set of features for which this feature is a parent
java.util.Set<Gff3FeatureImpl>	getCoFeatures() Get set of co-features.
java.util.Set<Gff3FeatureImpl>	getDescendents() Get set of all features descended from this features, through chains of Parent attributes.
java.util.Set<Gff3FeatureImpl>	getParents() Gets set of parent features
java.util.Set<Gff3FeatureImpl>	getTopLevelFeatures() Get the set of top level features from which this feature is descended
boolean	hasChildren()
boolean	hasCoFeatures()
int	hashCode()
boolean	hasParents()
boolean	isTopLevelFeature()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.tribble.gff.Gff3Feature

getAliases, getAttribute, getAttributes, getContig, getEnd, getID, getName, getPhase, getScore, getSource, getStart, getStrand, getType

Methods inherited from interface htsjdk.tribble.Feature

getChr

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Detail

Gff3FeatureImpl

public Gff3FeatureImpl(java.lang.String contig,
                       java.lang.String source,
                       java.lang.String type,
                       int start,
                       int end,
                       java.lang.Double score,
                       Strand strand,
                       int phase,
                       java.util.Map<java.lang.String,java.util.List<java.lang.String>> attributes)

Gff3FeatureImpl

public Gff3FeatureImpl(Gff3BaseData baseData)

Method Detail

getTopLevelFeatures

public java.util.Set<Gff3FeatureImpl> getTopLevelFeatures()

Get the set of top level features from which this feature is descended

Specified by:

getTopLevelFeatures in interface Gff3Feature

Returns:

set of top level feature from which this feature is descended

isTopLevelFeature

public boolean isTopLevelFeature()

Specified by:

isTopLevelFeature in interface Gff3Feature

getParents

public java.util.Set<Gff3FeatureImpl> getParents()

Gets set of parent features

Specified by:

getParents in interface Gff3Feature

Returns:

set of parent features

getChildren

public java.util.Set<Gff3FeatureImpl> getChildren()

Gets set of features for which this feature is a parent

Specified by:

getChildren in interface Gff3Feature

Returns:

set of child features

getBaseData

public Gff3BaseData getBaseData()

Description copied from interface: Gff3Feature

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

Specified by:

getBaseData in interface Gff3Feature

Returns:

getAncestors

public java.util.Set<Gff3FeatureImpl> getAncestors()

Get set of all features this feature descends from, through chains of Parent attributes. Derives_From can be used to specify a particular inheritance path for this feature when multiple paths are available

Specified by:

getAncestors in interface Gff3Feature

Returns:

set of ancestor features

getDescendents

public java.util.Set<Gff3FeatureImpl> getDescendents()

Get set of all features descended from this features, through chains of Parent attributes. Derives_From can be used to specify a particular inheritance path for this feature when multiple paths are available

Specified by:

getDescendents in interface Gff3Feature

Returns:

set of descendents

getCoFeatures

public java.util.Set<Gff3FeatureImpl> 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

Specified by:

getCoFeatures in interface Gff3Feature

Returns:

set of co-features

hasParents

public boolean hasParents()

Specified by:

hasParents in interface Gff3Feature

hasChildren

public boolean hasChildren()

Specified by:

hasChildren in interface Gff3Feature

hasCoFeatures

public boolean hasCoFeatures()

Specified by:

hasCoFeatures in interface Gff3Feature

addParent

public void addParent(Gff3FeatureImpl parent)

addCoFeature

public void addCoFeature(Gff3FeatureImpl coFeature)

Add a feature as a coFeature of this feature. When this method is called, the input coFeature will also be added as a coFeature of all the other coFeatures of this object, and this feature and all coFeatures will be added as coFeatures of the input coFeature. All coFeatures must have equal IDs and parents.

Parameters:

coFeature - feature to add as this features coFeature

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

flatten

public java.util.Set<Gff3FeatureImpl> flatten()

flatten this feature and all descendents into a set of features

Specified by:

flatten in interface Gff3Feature

Returns:

set of this feature and all descendents