Class HierarchyTree


  • public class HierarchyTree
    extends java.lang.Object
    A HierarchyTree holds the taxonomic information of a taxon.
    • Constructor Summary

      Constructors 
      Constructor Description
      HierarchyTree​(java.lang.String n, int taxid, java.lang.String rank, int leaves, int gIndex)  
      HierarchyTree​(java.lang.String n, int taxid, java.lang.String rank, int leaves, int gIndex, double copyNumber)
      Creates new HierarchyTree given the taxonomic information.
    • Constructor Detail

      • HierarchyTree

        public HierarchyTree​(java.lang.String n,
                             int taxid,
                             java.lang.String rank,
                             int leaves,
                             int gIndex,
                             double copyNumber)
        Creates new HierarchyTree given the taxonomic information.
      • HierarchyTree

        public HierarchyTree​(java.lang.String n,
                             int taxid,
                             java.lang.String rank,
                             int leaves,
                             int gIndex)
    • Method Detail

      • addParent

        public void addParent​(HierarchyTree p)
        Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.
      • getName

        public java.lang.String getName()
        Gets the name of the treenode.
      • getParent

        public HierarchyTree getParent()
        Gets the parent treenode.
      • getRank

        public java.lang.String getRank()
        Gets the rank of the treenode.
      • getTaxid

        public int getTaxid()
        Gets the taxon id of the treenode.
      • getSubclasses

        public java.util.List<HierarchyTree> getSubclasses()
        Gets the name of the treenode.
      • getSizeofSubclasses

        public int getSizeofSubclasses()
        Gets the list of the child treenodes.
      • getChild

        public HierarchyTree getChild​(java.lang.String name)
      • getLeaveCount

        public int getLeaveCount()
        Gets the size of sequence leaves directly belong to this treenode.
      • getGenusIndex

        public int getGenusIndex()
        Gets the index of the genus treenode in the genusNodeList. Returns -1 if not a genus node.
      • getCopyNumber

        public double getCopyNumber()
      • hasCopyNumberInfo

        public boolean hasCopyNumberInfo()
        Returns:
        true if the taxon has copy number information