Class HierarchyTree


  • public class HierarchyTree
    extends java.lang.Object
    • Constructor Detail

      • HierarchyTree

        public HierarchyTree​(java.lang.String n,
                             HierarchyTree p,
                             Taxonomy tax)
        Creates new HierarchyTree given the name and its parent
    • Method Detail

      • getName

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

        public HierarchyTree getParent()
        Gets the parent treenode
      • getSubclasses

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

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

        public HierarchyTree getSubclassbyName​(java.lang.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 java.io.IOException
        This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree
        Throws:
        java.io.IOException
      • unhideSeq

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

        public void hideSeq​(edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator iterator)
                     throws java.io.IOException
        This method hides a sequence by removing the words of that sequence from the total wordOccurrence
        Throws:
        java.io.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​(java.lang.String level,
                                java.util.List nodeList)
        get all the lowest level nodes in given hierarchy level starting from the given root
      • getNodeMap

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