Package org.snpeff.binseq

Class BinarySequence

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<BinarySequence>
    Direct Known Subclasses:
    DnaAndQualitySequence, DnaSequence, DnaSequencePe
    public abstract class BinarySequence
extends java.lang.Object
implements java.lang.Comparable<BinarySequence>, java.io.Serializable, java.lang.Cloneable
    Base class for a binary 'read'. I.e. a binary representation of a sequencer's read A read is a short DNA fragment (short now means anywhere from 36 bases to 10K).
    Author:
    pcingola
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      BinarySequence()  

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      BinarySequence clone()  
      char getBase​(int index)
      Return the base at position 'index'
      abstract int getCode​(int index)
      Return the code at position 'index'
      abstract Coder getCoder()
      Get sequence encoder & decoder
      abstract java.lang.String getSequence()
      Get the sequence as a String
      abstract int hashCode()  
      abstract int length()
      Get sequence length
      BinarySequence overlap​(BinarySequence sequence, int start)
      Creates a new sequence by overlapping 'this' and 'sequence' E.g.
      abstract BinarySequence read​(java.io.DataInputStream dataInStream)
      Read a sequence from a data stream
      protected abstract void readDataStream​(java.io.DataInputStream dataInStream)  
      abstract BinarySequence reverseWc()
      Reverse Watson-Cricks complement
      abstract void set​(java.lang.String seqStr)
      Set sequence from a string
      void setQuality​(int index, int quality)
      Set the quality at position 'index'
      abstract void write​(java.io.DataOutputStream dataOutStream)
      Write to a binary stream

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.lang.Comparable

        compareTo

    • Constructor Detail

      • BinarySequence

        public BinarySequence()

    • Method Detail

      • getBase

        public char getBase​(int index)
        Return the base at position 'index'

      • clone

        public BinarySequence clone()
        Overrides:
        clone in class java.lang.Object

      • getCode

        public abstract int getCode​(int index)
        Return the code at position 'index'

      • getCoder

        public abstract Coder getCoder()
        Get sequence encoder & decoder

      • getSequence

        public abstract java.lang.String getSequence()
        Get the sequence as a String

      • hashCode

        public abstract int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • length

        public abstract int length()
        Get sequence length

      • overlap

        public BinarySequence overlap​(BinarySequence sequence,
                              int start)
        Creates a new sequence by overlapping 'this' and 'sequence' E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO | other.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| this.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO | |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| Another case is when a sequence is fully included in the other sequence. In this case the result is just a copy of the longest sequence (with the quality updated) E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| other.sequence : | OOOOOOOOOOOOOOO | | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| this.sequence : | OOOOOOOOOOO | other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO| |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO|

      • read

        public abstract BinarySequence read​(java.io.DataInputStream dataInStream)
                             throws java.io.IOException
        Read a sequence from a data stream
        Throws:
        java.io.IOException

      • readDataStream

        protected abstract void readDataStream​(java.io.DataInputStream dataInStream)
                                throws java.io.IOException
        Throws:
        java.io.IOException

      • reverseWc

        public abstract BinarySequence reverseWc()
        Reverse Watson-Cricks complement

      • set

        public abstract void set​(java.lang.String seqStr)
        Set sequence from a string
        Parameters:
        seqStr -

      • setQuality

        public void setQuality​(int index,
                       int quality)
        Set the quality at position 'index'

      • write

        public abstract void write​(java.io.DataOutputStream dataOutStream)
                    throws java.io.IOException
        Write to a binary stream
        Throws:
        java.io.IOException