Class WindowedSequence<C extends Compound>

  • Type Parameters:
    C - The type of compound we return from a window
    All Implemented Interfaces:
    java.lang.Iterable<SequenceView<C>>

    public class WindowedSequence<C extends Compound>
    extends java.lang.Object
    implements java.lang.Iterable<SequenceView<C>>
    A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works. For each index requested we return a SequenceView or List of compounds back. If you perform a view on a Sequence whose length is not a multiple of the window the final window will be omitted i.e. if we have the sequence AGCGG and a window of 3 then you will only see AGC since GG exceeds the calculated length of this sequence. Because this does not implement a Sequence interface we do not recommend passing this class around. If you need to represent a windowed sequence as a real Sequence then translate it into a new Compound
    Author:
    ayates
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      SequenceView<C> get​(int index)
      Returns the window specified at the given index in offsets i.e.
      Sequence<C> getBackingSequence()
      Access the sequence which backs this window
      java.util.List<C> getCompounds​(int index)
      For a given position into the windowed view this will return those compounds we can see in the window.
      int getLength()
      Returns the size of the windowed sequence which is the length by the window size.
      int getWindowSize()
      Access the current window size
      java.util.Iterator<SequenceView<C>> iterator()
      Returns an iterator which will return the windows in a sequence in sequential order.
      protected int toStartIndex​(int index)
      Calculates start index according to the equation start = ( (index-1) - windowSize) +1
      • 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

      • WindowedSequence

        public WindowedSequence​(Sequence<C> sequence,
                                int windowSize)
    • Method Detail

      • getWindowSize

        public int getWindowSize()
        Access the current window size
      • getBackingSequence

        public Sequence<C> getBackingSequence()
        Access the sequence which backs this window
      • toStartIndex

        protected int toStartIndex​(int index)
        Calculates start index according to the equation start = ( (index-1) - windowSize) +1
      • getLength

        public int getLength()
        Returns the size of the windowed sequence which is the length by the window size. Trailing Compounds are omitted.
      • getCompounds

        public java.util.List<C> getCompounds​(int index)
        For a given position into the windowed view this will return those compounds we can see in the window. i.e. in the sequence AGGCCT requesting index 1 returns AGG and requesting index 2 return CCT.
        Parameters:
        index - Windowed index position
        Returns:
        The List of compounds
      • get

        public SequenceView<C> get​(int index)
        Returns the window specified at the given index in offsets i.e. asking for position 2 in a moving window sequence of size 3 will get you the window starting at position 4.
      • iterator

        public java.util.Iterator<SequenceView<C>> iterator()
        Returns an iterator which will return the windows in a sequence in sequential order.
        Specified by:
        iterator in interface java.lang.Iterable<C extends Compound>