Class Gene

  • All Implemented Interfaces:
    htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature, 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)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Gene.Transcript addTranscript​(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)  
      int compareTo​(Gene that)  
      boolean equals​(Object other)  
      Iterator<Gene.Transcript> iterator()  
      • Methods inherited from class htsjdk.samtools.util.Interval

        abuts, clone, compareTo, countBases, equalsWithStrandAndName, getContig, getEnd, getIntersectionLength, getName, getSequence, getStart, getStrand, hashCode, intersect, intersects, isNegativeStrand, isPositiveStrand, length, pad, toString
      • Methods inherited from interface htsjdk.tribble.Feature

        getChr
      • Methods inherited from interface htsjdk.samtools.util.Locatable

        contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf
    • 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