Class HierarchyTree

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

public class HierarchyTree extends Object
  • Constructor Details

    • HierarchyTree

      public HierarchyTree(String n, HierarchyTree p, Taxonomy tax)
      Creates new HierarchyTree given the name and its parent
  • Method Details

    • getName

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

      public HierarchyTree getParent()
      Gets the parent treenode
    • getSubclasses

      public Collection<HierarchyTree> getSubclasses()
      Gets the array of the subclasses if any
    • getLeaves

      public Collection getLeaves()
      Gets the array of Sequenceleaves if any
    • getSubclassbyName

      public HierarchyTree getSubclassbyName(String n)
      Gets the subclass with the given name
    • getSizeofChildren

      public int getSizeofChildren()
      Gets the size of the children
    • getSizeofSubclasses

      public int getSizeofSubclasses()
      Gets the size of the subclasses
    • getSizeofLeaves

      public int getSizeofLeaves()
      Gets the size of sequence leaves directly belong to this tree, not including the hidden leaves
    • initWordOccurrence

      public void initWordOccurrence(LineageSequence pSeq, float[] wordPriorArr, boolean initWordOccurrence) throws IOException
      This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree
      Throws:
      IOException
    • unhideSeq

      public void unhideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator) throws IOException
      This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree
      Throws:
      IOException
    • hideSeq

      public void hideSeq(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator) throws IOException
      This method hides a sequence by removing the words of that sequence from the total wordOccurrence
      Throws:
      IOException
    • changeParentSeqCount

      public void changeParentSeqCount(int i)
    • isWordOccurDone

      public boolean isWordOccurDone()
    • getWordOccurrenceSize

      public int getWordOccurrenceSize()
    • getNumberofUniqueWords

      public int getNumberofUniqueWords()
    • createWordOccurrenceFromSubclasses

      public void createWordOccurrenceFromSubclasses()
      creates the word occurrence array from its children if the word occurrence for this node does not exist
    • getWordOccurrence

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

      public int getNumOfLeaves()
      Counts the number of sequence leaves below this tree
    • increTotalSeqs

      public void increTotalSeqs()
    • getTotalSeqs

      public int getTotalSeqs()
    • getMissCount

      public int getMissCount()
    • getNumTotalTestedseq

      public int getNumTotalTestedseq()
    • incNumTotalTestedseq

      public void incNumTotalTestedseq()
    • incMissCount

      public void incMissCount()
    • getTaxonomy

      public Taxonomy getTaxonomy()
    • isSingleton

      public boolean isSingleton()
    • getNodeList

      public void getNodeList(String level, List nodeList)
      get all the lowest level nodes in given hierarchy level starting from the given root
    • getNodeMap

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