Class RawHierarchyTree

java.lang.Object
edu.msu.cme.rdp.classifier.train.RawHierarchyTree

public class RawHierarchyTree extends Object
A RawHierarchyTree holds the raw taxon and sequences information. A RawHierarchyTree can only have one type of children: child treenodes or child sequences.
  • Constructor Details

    • RawHierarchyTree

      public RawHierarchyTree(String n, RawHierarchyTree p, Taxonomy tax)
      Creates new RawHierarchyTree given the name and its parent. Note: a RawHierarchyTree can only have one type of children: child treenodes or child sequences. Usually the lowest ranked nodes contain the sequence leaves.
  • Method Details

    • setCopyNumber

      protected void setCopyNumber(float c)
    • getCopyNumber

      public float getCopyNumber()
    • hasCopyNumber

      public boolean hasCopyNumber()
    • getName

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

      public RawHierarchyTree getParent()
      Gets the parent treenode.
    • getSubclasses

      public Collection<RawHierarchyTree> getSubclasses()
      Gets the array of the subclasses if any.
    • getSubclassbyName

      public RawHierarchyTree getSubclassbyName(String n)
      Gets the child treenode with the given name.
    • getSizeofChildren

      public int getSizeofChildren()
      Gets the size of the children, either taxon children or sequence leaves.
    • getSizeofSubclasses

      public int getSizeofSubclasses()
      Gets the size of the child treenodes.
    • initWordOccurrence

      public void initWordOccurrence(LineageSequence pSeq, float[] wordPriorArr) throws IOException
      This method initiates the word occurrences from a sequence for the lowest level of the hierarchy tree. Duplicate words from one sequence will be count only once.
      Throws:
      IOException
    • getWordOccurrenceSize

      public int getWordOccurrenceSize()
      Returns the size of the array wordOccurrence.
    • getWordOccurrence

      public int getWordOccurrence(int wordIndex)
      Gets the word occurrence for the given word index.
    • releaseWordOccurrence

      public void releaseWordOccurrence()
      Resets the array wordOccurrence to null.
    • getLeaveCount

      public int getLeaveCount()
      Counts the number of sequence leaves below this tree.
    • getGenusNodeCount

      public int getGenusNodeCount()
    • isSingleton

      public boolean isSingleton()
    • getNonSingletonLeaveCount

      public int getNonSingletonLeaveCount()
      Counts the number of non-singleton sequence leaves below this tree.
    • getTaxonomy

      public Taxonomy getTaxonomy()
      Returns the taxon object of this treenode.
    • setGenusIndex

      public void setGenusIndex(int i)
      Sets the genus index of this treenode.
    • getGenusIndex

      public int getGenusIndex()
      Returns the genus index of this treenode.
    • getNodeMap

      public void getNodeMap(String level, HashMap<String,RawHierarchyTree> nodeMap)
      get all the lowest level nodes in given hierarchy level starting from the given root