Package org.snpeff.motif

Class Pwm

  • Direct Known Subclasses:
    PwmAndSeqs
    public class Pwm
extends java.lang.Object
    Create a DNA motif count matrix Refrence http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
    Author:
    pcingola

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static char[] BASES  
      static int SCALE  

    • Constructor Summary

      Constructors 
      Constructor Description
      Pwm​(int length)  
      Pwm​(java.lang.String file)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void calcLogOddsWeight()
      Calculate log odds matrix from counts Reference: http://en.wikipedia.org/wiki/Position-specific_scoring_matrix
      char[] getBestSequence()
      Get best matching sequence (highest score)
      java.lang.String getBestSequenceStr()  
      int getCount​(char base, int position)
      Get counts for a given position
      java.lang.String getId()  
      double getLogOdds​(char base, int position)  
      java.lang.String getName()  
      int getTotalCount()  
      boolean isConserved​(int pos)
      Is position 'pos' conserved (only one base has non-zero counts)
      int length()  
      double score​(java.lang.String dna)
      Calculate PWM score for a string
      void set​(java.lang.String dna)
      Set PWM as a perfect match to a dna sequence
      void setCounts​(char base, int[] counts)
      Set counts for one base
      void setId​(java.lang.String id)  
      void setName​(java.lang.String name)  
      java.lang.String toString()  
      void updateCounts​(java.lang.String dna)  
      void updateCounts​(java.lang.String dna, int inc)
      Update counts matrix.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

      • BASES

        public static final char[] BASES

    • Constructor Detail

      • Pwm

        public Pwm​(int length)

      • Pwm

        public Pwm​(java.lang.String file)

    • Method Detail

      • calcLogOddsWeight

        public void calcLogOddsWeight()
        Calculate log odds matrix from counts Reference: http://en.wikipedia.org/wiki/Position-specific_scoring_matrix

      • getBestSequence

        public char[] getBestSequence()
        Get best matching sequence (highest score)
        Returns:

      • getBestSequenceStr

        public java.lang.String getBestSequenceStr()

      • getCount

        public int getCount​(char base,
                    int position)
        Get counts for a given position

      • getId

        public java.lang.String getId()

      • getLogOdds

        public double getLogOdds​(char base,
                         int position)

      • getName

        public java.lang.String getName()

      • getTotalCount

        public int getTotalCount()

      • isConserved

        public boolean isConserved​(int pos)
        Is position 'pos' conserved (only one base has non-zero counts)

      • length

        public int length()

      • score

        public double score​(java.lang.String dna)
        Calculate PWM score for a string

      • set

        public void set​(java.lang.String dna)
        Set PWM as a perfect match to a dna sequence

      • setCounts

        public void setCounts​(char base,
                      int[] counts)
        Set counts for one base

      • setId

        public void setId​(java.lang.String id)

      • setName

        public void setName​(java.lang.String name)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • updateCounts

        public void updateCounts​(java.lang.String dna)

      • updateCounts

        public void updateCounts​(java.lang.String dna,
                         int inc)
        Update counts matrix.