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

WindowedSequence

public WindowedSequence(Sequence<C> sequence,
 int windowSize)

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>