Package picard.annotation

Class Gene

  • All Implemented Interfaces:
    htsjdk.samtools.util.Locatable, Cloneable, Comparable<htsjdk.samtools.util.Interval>, Iterable<Gene.Transcript>
    public class Gene
extends htsjdk.samtools.util.Interval
implements Iterable<Gene.Transcript>
    Holds annotation of a gene for storage in an OverlapDetector. May hold multiple transcripts for the same gene. The transcripts must all be relative to the same strand.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      class  Gene.Transcript
      A single transcript of a gene.

    • Constructor Summary

      Constructors 
      Constructor Description
      Gene​(String sequence, int start, int end, boolean negative, String name)  

    • Constructor Detail

      • Gene

        public Gene​(String sequence,
            int start,
            int end,
            boolean negative,
            String name)

    • Method Detail

      • addTranscript

        public Gene.Transcript addTranscript​(String name,
                                     int transcriptionStart,
                                     int transcriptionEnd,
                                     int codingStart,
                                     int codingEnd,
                                     int numExons)

      • compareTo

        public int compareTo​(Gene that)

      • equals

        public boolean equals​(Object other)
        Overrides:
        equals in class htsjdk.samtools.util.Interval