Class SequenceRegion

java.lang.Object
htsjdk.tribble.gff.SequenceRegion
All Implemented Interfaces:
Locatable
public class SequenceRegion extends Object implements Locatable
Represents a sequence region feature in a gff3 file. May be linear or circular.

  • Method Details

    • getContig

      public 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

      public int getStart()
      Specified by:
      getStart in interface Locatable
      Returns:
      1-based start position, undefined if getContig() == null

    • getEnd

      public int getEnd()
      Specified by:
      getEnd in interface Locatable
      Returns:
      1-based closed-ended position, undefined if getContig() == null

    • isCircular

      public boolean isCircular()

    • equals

      public boolean equals(Object other)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object