Class RawHierarchyTree


  • public class RawHierarchyTree
    extends java.lang.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 Detail

      • RawHierarchyTree

        public RawHierarchyTree​(java.lang.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 Detail

      • setCopyNumber

        protected void setCopyNumber​(float c)
      • getCopyNumber

        public float getCopyNumber()
      • hasCopyNumber

        public boolean hasCopyNumber()
      • getName

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

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

        public RawHierarchyTree getSubclassbyName​(java.lang.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 java.io.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:
        java.io.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​(java.lang.String level,
                               java.util.HashMap<java.lang.String,​RawHierarchyTree> nodeMap)
        get all the lowest level nodes in given hierarchy level starting from the given root