Class HierarchyTree

java.lang.Object
edu.msu.cme.rdp.classifier.HierarchyTree

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

    • HierarchyTree

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

      public HierarchyTree(String n, int taxid, String rank, int leaves, int gIndex)
  • Method Details

    • addParent

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

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

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

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

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

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

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

      public HierarchyTree getChild(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