org.biojava3.core.sequence.views
Class WindowedSequence<C extends Compound>

java.lang.Object
  extended by org.biojava3.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
WindowedSequence(Sequence<C> sequence, int windowSize)
           
 
Method Summary
 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
 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
 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
 

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 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<SequenceView<C extends Compound>>