Package org.snpeff.complexity

Class SequenceComplexity

  • public class SequenceComplexity
extends java.lang.Object
    Measures the complexity of a sequence Ideally we'd like to measure the Kolmogorov complexity of the sequence. Unfortunately it is not a computable function (see http://en.wikipedia.org/wiki/Kolmogorov_complexity)
    Author:
    pcingola

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int complexity​(java.lang.String seq)
      Measure string's complexity
      double ratio​(java.lang.String seq)
      Measure string's complexity ratio.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • SequenceComplexity

        public SequenceComplexity()

    • Method Detail

      • complexity

        public int complexity​(java.lang.String seq)
        Measure string's complexity

      • ratio

        public double ratio​(java.lang.String seq)
        Measure string's complexity ratio. I.e. complexity(seq) / seq.length