Class MCTaxon

  • Direct Known Subclasses:
    UnifracTaxon

    public class MCTaxon
    extends edu.msu.cme.rdp.taxatree.Taxon
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int Count_Array_size  
      protected java.util.Map<MCSample,​double[]> sampleCountMap  
      • Fields inherited from class edu.msu.cme.rdp.taxatree.Taxon

        ROOT_TAXON
      • Fields inherited from class edu.msu.cme.rdp.taxatree.Node

        taxid
    • Constructor Summary

      Constructors 
      Constructor Description
      MCTaxon​(int id, java.lang.String name, java.lang.String rank)  
      MCTaxon​(int id, java.lang.String name, java.lang.String rank, boolean unclassified)  
      MCTaxon​(edu.msu.cme.rdp.taxatree.Taxon t)  
    • Field Detail

      • sampleCountMap

        protected java.util.Map<MCSample,​double[]> sampleCountMap
    • Constructor Detail

      • MCTaxon

        public MCTaxon​(int id,
                       java.lang.String name,
                       java.lang.String rank)
      • MCTaxon

        public MCTaxon​(int id,
                       java.lang.String name,
                       java.lang.String rank,
                       boolean unclassified)
      • MCTaxon

        public MCTaxon​(edu.msu.cme.rdp.taxatree.Taxon t)
    • Method Detail

      • addSequence

        public void addSequence​(java.lang.String seqid)
      • getSequences

        public java.util.Set<java.lang.String> getSequences()
      • setLineage

        public void setLineage​(java.lang.String lineage)
      • getLineage

        public java.lang.String getLineage()
      • getSamples

        public java.util.Set<MCSample> getSamples()
      • getCount

        public double getCount​(MCSample s)
      • getCopyCorrectedCount

        public double getCopyCorrectedCount​(MCSample s)
      • incCount

        public void incCount​(MCSample s,
                             double c)
      • incCount

        public void incCount​(MCSample s,
                             double c,
                             double copyNumber)