Package org.broadinstitute.hellbender.utils.codecs.refseq

Interface RefSeqTranscript

All Superinterfaces:
htsjdk.samtools.util.Locatable
All Known Implementing Classes:
RefSeqFeature
public interface RefSeqTranscript extends htsjdk.samtools.util.Locatable
Created by IntelliJ IDEA. User: asivache Date: Sep 22, 2009 Time: 5:22:30 PM To change this template use File | Settings | File Templates.

  • Method Summary

    Modifier and Type
    Method
    Description
    SimpleInterval
    getCodingLocation()
    Returns genomic interval of the coding sequence (does not include UTRs, but still includes introns, since it's a single interval on the DNA)
    List<SimpleInterval>
    getExons()
    Returns the list of all exons in this transcript, as genomic intervals
    String
    getGeneName()
    Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc, but the implementation can decide otherwise)
    SimpleInterval
    getLocation()
    Returns transcript's full genomic interval (includes all exons with UTRs)
    int
    getStrand()
    Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively
    String
    getTranscriptId()
    Returns id of the transcript (RefSeq NM_* id)

    Methods inherited from interface htsjdk.samtools.util.Locatable

    contains, contigsMatch, getContig, getEnd, getLengthOnReference, getStart, overlaps, withinDistanceOf

  • Method Details

    • getTranscriptId

      String getTranscriptId()
      Returns id of the transcript (RefSeq NM_* id)

    • getStrand

      int getStrand()
      Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively

    • getLocation

      SimpleInterval getLocation()
      Returns transcript's full genomic interval (includes all exons with UTRs)

    • getCodingLocation

      SimpleInterval getCodingLocation()
      Returns genomic interval of the coding sequence (does not include UTRs, but still includes introns, since it's a single interval on the DNA)

    • getGeneName

      String getGeneName()
      Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc, but the implementation can decide otherwise)

    • getExons

      List<SimpleInterval> getExons()
      Returns the list of all exons in this transcript, as genomic intervals