Class Gene.Transcript

java.lang.Object
picard.annotation.Gene.Transcript
Enclosing class:
Gene

public class Gene.Transcript extends Object
A single transcript of a gene. Sequence name is stored in the enclosing object (class Gene).
  • Field Details

    • name

      public final String name
    • transcriptionStart

      public final int transcriptionStart
    • transcriptionEnd

      public final int transcriptionEnd
    • codingStart

      public final int codingStart
    • codingEnd

      public final int codingEnd
    • exons

      public final Gene.Transcript.Exon[] exons
  • Constructor Details

    • Transcript

      public Transcript(String name, int transcriptionStart, int transcriptionEnd, int codingStart, int codingEnd, int numExons)
  • Method Details

    • addExon

      public Gene.Transcript.Exon addExon(int start, int end)
    • start

      public int start()
    • end

      public int end()
    • length

      public int length()
    • isSoloTranscript

      public boolean isSoloTranscript()
    • getGene

      public Gene getGene()
    • assignLocusFunctionForRange

      public void assignLocusFunctionForRange(int start, LocusFunction[] locusFunctions)
      Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript. Does not overwrite an existing value in locusFunctions that is stronger than the function for that locus in this transcript.
      Parameters:
      start - 1-based genomic coordinate of the first position in locusFunctions.
      locusFunctions -
    • addCoverageCounts

      public void addCoverageCounts(int genomeStart, int genomeEnd, int[] coverage)
      Parameters:
      genomeStart -
      genomeEnd -
      coverage -
    • getTranscriptCoordinate

      public int getTranscriptCoordinate(int genomeCoordinate)
      Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object