Gff3Feature (htsjdk 3.0.5 API)

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

All Methods Instance Methods Abstract Methods Default Methods
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.util.List<java.lang.String>`	`getAliases()`
`java.util.Set<? extends Gff3Feature>`	`getAncestors()` Get set of all features this feature descends from, through chains of Parent attributes.
`default java.util.List<java.lang.String>`	`getAttribute(java.lang.String key)`
`default java.util.Map<java.lang.String,java.util.List<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 double`	`getScore()`
`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.util.List<java.lang.String> getAttribute(java.lang.String key)
```
  - getAttributes
```
default java.util.Map<java.lang.String,java.util.List<java.lang.String>> getAttributes()
```
  - getID
```
default java.lang.String getID()
```
  - getName
```
default java.lang.String getName()
```
  - getAliases
```
default java.util.List<java.lang.String> getAliases()
```
  - getScore
```
default double getScore()
```
  - 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()
```

Interface Gff3Feature

Method Summary

Methods inherited from interface htsjdk.tribble.Feature

Methods inherited from interface htsjdk.samtools.util.Locatable

Method Detail

getTopLevelFeatures

isTopLevelFeature

getSource

getEnd

getStrand

getPhase

getType

getContig

getStart

getAttribute

getAttributes

getID

getName

getAliases

getScore

getBaseData

getParents

getChildren

getAncestors

getDescendents

getCoFeatures

flatten

hasParents

hasChildren

hasCoFeatures