Package org.snpeff.motif

Class Jaspar

  • All Implemented Interfaces:
    java.lang.Iterable<Pwm>
    public class Jaspar
extends java.lang.Object
implements java.lang.Iterable<Pwm>
    Load PWM matrices from a Jaspar file
    Author:
    pablocingolani

    • Constructor Summary

      Constructors 
      Constructor Description
      Jaspar()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Pwm getPwm​(java.lang.String pwmId)  
      java.util.Iterator<Pwm> iterator()  
      void load​(java.lang.String jasparMatrixFile)
      Load matrix file
      void setVerbose​(boolean verbose)  

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Constructor Detail

      • Jaspar

        public Jaspar()

    • Method Detail

      • getPwm

        public Pwm getPwm​(java.lang.String pwmId)

      • iterator

        public java.util.Iterator<Pwm> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<Pwm>

      • load

        public void load​(java.lang.String jasparMatrixFile)
        Load matrix file
        Parameters:
        jasparMatrixFile -

      • setVerbose

        public void setVerbose​(boolean verbose)