Package org.biojava.nbio.core.sequence.views

Class WindowedSequence<C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.views.WindowedSequence<C>
Type Parameters:
C - The type of compound we return from a window
All Implemented Interfaces:
Iterable<SequenceView<C>>
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
Author:
ayates

  • Constructor Summary

    Constructors
    Constructor
    Description
    WindowedSequence(Sequence<C> sequence, int windowSize)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    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.
    Sequence<C>
    getBackingSequence()
    Access the sequence which backs this window
    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.
    int
    getLength()
    Returns the size of the windowed sequence which is the length by the window size.
    int
    getWindowSize()
    Access the current window size
    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 Details

  • Method Details

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