Class 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 Detail

      • 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
    • Constructor Detail

      • Transcript

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

      • 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.
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object