Class TreeFactory

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

public class TreeFactory extends Object
  • Constructor Details

  • Method Details

    • buildTree

      public void buildTree()
      build the taxonomic tree without sequences attached to it
    • addSequence

      public HierarchyTree addSequence(LineageSequence pSeq) throws IOException
      For the given sequence name, its ancestors, and the sequence, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent. If the root is already exist, checks the ParsedSequence to see if its oldest ancestor is the same as the previous root.
      Throws:
      IOException
    • addSequence

      public HierarchyTree addSequence(LineageSequence pSeq, boolean initWordOccurrence) throws IOException
      Throws:
      IOException
    • getTaxonomy

      public Taxonomy getTaxonomy(String seqName, String ancestorName, int pid, int index)
    • getRoot

      public HierarchyTree getRoot()
      Gets the root of the tree
    • getRankSet

      public Set<String> getRankSet()
    • getLowestRank

      public String getLowestRank()
    • displayTreePhylo

      public void displayTreePhylo(HierarchyTree root, String index, int indent)
      display the phylogenetic tree for each node, display the index and the name for each sequence, diaplay the name and the description
    • calculateWordPrior

      public void calculateWordPrior()
    • printWordPriors

      public void printWordPriors() throws IOException
      Throws:
      IOException
    • getWordPrior

      public float getWordPrior(int wordIndex)