Package 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 Details

    • getTopLevelFeatures

      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 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 String getType()

    • getContig

      default 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 List<String> getAttribute(String key)

    • getAttributes

      default Map<String,List<String>> getAttributes()

    • getID

      default String getID()

    • getName

      default String getName()

    • getAliases

      default List<String> getAliases()

    • getScore

      default double getScore()

    • getBaseData

      Gff3BaseData getBaseData()
      Get BaseData object which contains all the basic information of the feature
      Returns:

    • getParents

      Set<? extends Gff3Feature> getParents()
      Gets set of parent features
      Returns:
      set of parent features

    • getChildren

      Set<? extends Gff3Feature> getChildren()
      Gets set of features for which this feature is a parent
      Returns:
      set of child features

    • getAncestors

      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

      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

      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

      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()