Class DnaSequencePe

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<BinarySequence>

    public class DnaSequencePe
    extends BinarySequence
    Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
    Author:
    pcingola
    See Also:
    Serialized Form
    • Field Detail

      • coder

        public static final Coder coder
    • Constructor Detail

      • DnaSequencePe

        public DnaSequencePe​(java.lang.String seqStr)
      • DnaSequencePe

        public DnaSequencePe​(java.lang.String seqStr1,
                             java.lang.String seqStr2,
                             int gap)
    • Method Detail

      • getCode

        public int getCode​(int index)
        Description copied from class: BinarySequence
        Return the code at position 'index'
        Specified by:
        getCode in class BinarySequence
      • getGap

        public int getGap()
      • intLen

        public int intLen​(int len)
        Calculate the length of a sequence
        Parameters:
        len -
        Returns:
      • read

        public DnaSequencePe read​(java.io.DataInputStream dataInStream)
                           throws java.io.IOException
        Read data in binary format
        Specified by:
        read in class BinarySequence
        Parameters:
        dataOutStream -
        Throws:
        java.io.IOException
      • readDataStream

        protected void readDataStream​(java.io.DataInputStream dataInStream)
                               throws java.io.IOException
        Read data in binary format
        Specified by:
        readDataStream in class BinarySequence
        Parameters:
        dataOutStream -
        Throws:
        java.io.IOException
      • set

        public void set​(java.lang.String seqStr)
        Description copied from class: BinarySequence
        Set sequence from a string
        Specified by:
        set in class BinarySequence
      • setGap

        public void setGap​(int gap)
      • toString

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

        public void write​(java.io.DataOutputStream dataOutStream)
                   throws java.io.IOException
        Write data in binary format
        Specified by:
        write in class BinarySequence
        Parameters:
        dataOutStream -
        Throws:
        java.io.IOException