Package org.snpeff.spliceSites

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)