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

Method Summary

Methods

Modifier and Type	Method and 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
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>>