Package org.biojava.nbio.core.sequence

Class CDSSequence

java.lang.Object
org.biojava.nbio.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava.nbio.core.sequence.DNASequence
org.biojava.nbio.core.sequence.CDSSequence
All Implemented Interfaces:
Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>
public class CDSSequence extends DNASequence
Represents a exon or coding sequence in a gene. It has a parent TranscriptSequence where a TranscriptSequence is the child of a GeneSequence Not important for protein construction but the phase is used if outputting the gene to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
Author:
Scooter Willis

  • Constructor Details

    • CDSSequence

      public CDSSequence(TranscriptSequence parentSequence, int bioBegin, int bioEnd, int phase)
      Parameters:
      parentSequence -
      bioBegin -
      bioEnd -
      phase -

  • Method Details

    • getLength

      public int getLength()
      Description copied from interface: Sequence
      Returns the length of the Sequence
      Specified by:
      getLength in interface Sequence<NucleotideCompound>
      Overrides:
      getLength in class AbstractSequence<NucleotideCompound>

    • getPhase

      public Integer getPhase()
      Returns:
      get the phase

    • getStrand

      public Strand getStrand()
      Returns:
      get the strand

    • getCodingSequence

      public String getCodingSequence()
      A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence. When getting a ProteinSequence from a TranscriptSequence this method is callled for each CDSSequence {@link http://www.sequenceontology.org/gff3.shtml} {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
      Returns:
      coding sequence