PwmAndSeqs (SnpEff 5.1 API)

java.lang.Object

org.snpeff.motif.Pwm

org.snpeff.motif.PwmAndSeqs

public class PwmAndSeqs extends Pwm

Create a DNA motif count matrix and also count the number of sequences in that contribute to this motif.

Author:: pcingola

Field Summary

Fields inherited from class org.snpeff.motif.Pwm
BASES, SCALE
Constructor Summary

Constructors

Constructor

Description

PwmAndSeqs(int len)
Method Summary

Modifier and Type

Method

Description

String

toString()

void

updateCounts(String dna, int inc, long rsId)

Update counts matrix.

Methods inherited from class org.snpeff.motif.Pwm
calcLogOddsWeight, getBestSequence, getBestSequenceStr, getCount, getId, getLogOdds, getName, getTotalCount, isConserved, length, score, set, setCounts, setId, setName, updateCounts, updateCounts

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- PwmAndSeqs
  
  public PwmAndSeqs(int len)
Method Details
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Pwm
- updateCounts
  
  public void updateCounts(String dna, int inc, long rsId)
  
  Update counts matrix.
  
  Parameters:
  
  dna -