Package htsjdk.samtools.util

Interface Locatable

All Known Subinterfaces:
BEDFeature, Feature, Gff3Feature
All Known Implementing Classes:
AbstractLocusInfo, BAMRecord, FullBEDFeature, Gff3FeatureImpl, Interval, MutableFeature, SamLocusIterator.LocusInfo, SAMRecord, SAMSequenceRecord, SequenceRegion, SimpleBEDFeature, SimpleFeature, SRALazyRecord, VariantContext
public interface Locatable
Any class that has a single logical mapping onto the genome should implement Locatable positions should be reported as 1-based and closed at both ends

  • Method Summary

    Modifier and Type
    Method
    Description
    default boolean
    contains(Locatable other)
    Determines whether this interval contains the entire region represented by other (in other words, whether it covers it).
    default boolean
    contigsMatch(Locatable other)
    Determine if this is on the same contig as other this must be equivalent to this.getContig().equals(other.getContig()) but may be implemented more efficiently
    String
    getContig()
    Gets the contig name for the contig this is mapped to.
    int
    getEnd()
     
    default int
    getLengthOnReference()
     
    int
    getStart()
     
    default boolean
    overlaps(Locatable other)
    Determines whether this interval overlaps the provided locatable.
    default boolean
    withinDistanceOf(Locatable other, int distance)
    Determines whether this interval comes within distance of overlapping the provided locatable.

  • Method Details

    • getContig

      String getContig()
      Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.
      Returns:
      name of the contig this is mapped to, potentially null

    • getStart

      int getStart()
      Returns:
      1-based start position, undefined if getContig() == null

    • getEnd

      int getEnd()
      Returns:
      1-based closed-ended position, undefined if getContig() == null

    • getLengthOnReference

      default int getLengthOnReference()
      Returns:
      number of bases of reference covered by this interval

    • overlaps

      default boolean overlaps(Locatable other)
      Determines whether this interval overlaps the provided locatable.
      Parameters:
      other - interval to check
      Returns:
      true if this interval overlaps other, otherwise false

    • withinDistanceOf

      default boolean withinDistanceOf(Locatable other, int distance)
      Determines whether this interval comes within distance of overlapping the provided locatable. When distance = 0 this is equal to overlaps(Locatable)
      Parameters:
      other - interval to check
      distance - how many bases may be between the two intervals for us to still consider them overlapping.
      Returns:
      true if this interval overlaps other, otherwise false

    • contains

      default boolean contains(Locatable other)
      Determines whether this interval contains the entire region represented by other (in other words, whether it covers it).
      Parameters:
      other - interval to check
      Returns:
      true if this interval contains all of the base positions spanned by other, otherwise false

    • contigsMatch

      default boolean contigsMatch(Locatable other)
      Determine if this is on the same contig as other this must be equivalent to this.getContig().equals(other.getContig()) but may be implemented more efficiently
      Returns:
      true iff this.getContig().equals(other.getContig())