Class WindowedSequence<C extends Compound>

  • Type Parameters:
    C - The type of compound we return from a window
    All Implemented Interfaces:

    public class WindowedSequence<C extends Compound>
    extends Object
    implements 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
    • Method Detail

      • getWindowSize

        public int getWindowSize()
        Access the current window size
      • 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 List<CgetCompounds​(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.
        index - Windowed index position
        The List of compounds
      • get

        public SequenceView<Cget​(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.