Class DnaNSequence

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

    public class DnaNSequence
    extends DnaSequence
    Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • DnaNSequence

        public DnaNSequence​(int length,
                            long[] codes)
      • DnaNSequence

        public DnaNSequence​(java.lang.String seqStr)
    • Method Detail

      • empty

        public static DnaNSequence empty()
        Empty sequence singleton
      • getBase

        public char getBase​(int index)
        Description copied from class: BinarySequence
        Return the base at position 'index'
        Overrides:
        getBase in class DnaSequence
      • getBases

        public java.lang.String getBases​(int index,
                                         int len)
        Get a few bases from this sequence
        Overrides:
        getBases in class DnaSequence
      • read

        public BinarySequence read​(java.io.DataInputStream dataInStream)
                            throws java.io.IOException
        Read data in binary format
        Overrides:
        read in class DnaSequence
        Throws:
        java.io.IOException
      • readDataStream

        protected void readDataStream​(java.io.DataInputStream dataInStream)
                               throws java.io.IOException
        Read data in binary format
        Overrides:
        readDataStream in class DnaSequence
        Throws:
        java.io.IOException
      • set

        public void set​(java.lang.String seqStr)
        Description copied from class: DnaSequence
        Set sequence
        Overrides:
        set in class DnaSequence
      • setBase

        public void setBase​(int index,
                            char base)
        Replace a base in the sequence
        Overrides:
        setBase in class DnaSequence
      • write

        public void write​(java.io.DataOutputStream dataOutStream)
                   throws java.io.IOException
        Write data in binary format
        Overrides:
        write in class DnaSequence
        Throws:
        java.io.IOException