Package picard.annotation

Class Gene

java.lang.Object
htsjdk.samtools.util.Interval
picard.annotation.Gene
All Implemented Interfaces:
htsjdk.samtools.util.Locatable, htsjdk.tribble.Feature, htsjdk.tribble.NamedFeature, 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

    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 class java.lang.Object

    finalize, getClass, notify, notifyAll, wait, wait, wait

    Methods inherited from interface htsjdk.tribble.Feature

    getChr

    Methods inherited from interface java.lang.Iterable

    forEach, spliterator

    Methods inherited from interface htsjdk.samtools.util.Locatable

    contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

  • Constructor Details

    • Gene

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

  • Method Details

    • addTranscript

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

    • iterator

      public Iterator<Gene.Transcript> iterator()
      Specified by:
      iterator in interface Iterable<Gene.Transcript>

    • compareTo

      public int compareTo(Gene that)

    • equals

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