Class AcgtTree

java.lang.Object
org.snpeff.spliceSites.AcgtTree

public class AcgtTree extends Object
ACGT tree
Author:
pcingola
  • Field Details

    • BASES

      public static final char[] BASES
    • LOG2

      public static final double LOG2
    • FAKE_COUNTS

      public static final int FAKE_COUNTS
      See Also:
    • MAX_ENTROPY

      public static final double MAX_ENTROPY
      See Also:
  • Constructor Details

    • AcgtTree

      public AcgtTree()
    • AcgtTree

      protected AcgtTree(String name, AcgtTree parent)
  • Method Details

    • base2index

      public static int base2index(char base)
    • add

      public void add(String sequence)
    • entropy

      public double entropy()
      Calculate the entropy
    • entropyAll

      public List<Double> entropyAll(int thresholdCount)
    • findNodeNames

      public List<String> findNodeNames(double thresholdEntropy, double thresholdP, int thresholdCount)
      Find node names that are within the thresholds
    • get

      public AcgtTree get(char base)
      Get a node
    • get

      public AcgtTree get(String bases)
      Get node indexed by this string
    • getOrCreate

      public AcgtTree getOrCreate(char base)
      Get a node (create it if it doesn't exist)
    • getTotalCount

      public int getTotalCount()
    • inc

      public void inc(char base)
      Increment counter for a base
    • pAll

      public List<Double> pAll(int thresholdCount)
    • pAll

      protected void pAll(int thresholdCount, List<Double> ps)
    • seqConservation

      public double seqConservation()
    • set

      public void set(char base, AcgtTree n)
      Set a node
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • toString

      public String toString(String tabs, double thresholdEntropy, double thresholdP, int thresholdCount)