Package picard.annotation

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