org.biojava.nbio.genome.parsers.gff

Class LocIterator

java.lang.Object

org.biojava.nbio.genome.parsers.gff.LocIterator

All Implemented Interfaces:

Iterator<Location>

public class LocIterator
extends Object
implements Iterator<Location>

Move a sliding window over a Location. Window size and increment can be specified. If the increment is negative, the iteration starts at end of Location and moves toward beginning.

Author:

Hanno Hinsch

Constructor Summary

Constructors

Constructor and Description
LocIterator(Location bounds, int windowSize, int increment) Construct an iterator that slides a window over a Location.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	hasNext() Check if next window of default size is available.
boolean	hasNext(int windowSize, int increment) Check if next window of specified size is available.
static void	main(String[] args) Deprecated.
Location	next() Get next window of default size, then increment position by default amount.
Location	next(int windowSize, int increment) Get next window of specified size, then increment position by specified amount.
Location	remainder() Get portion of bounding location that has not yet been retrieved by next() method.
void	remove() Unsupported.
String	toString() Get string representation of iterator.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

LocIterator

public LocIterator(Location bounds,
           int windowSize,
           int increment)

Construct an iterator that slides a window over a Location.

Parameters:

bounds - The location over which to iterate.

windowSize - The size of the moving window.

increment - The increment by which to move the window at each iteration. If increment is positive, the iteration starts at the beginning of the bounding location and moves toward the end; if the increment is negative, the iteration starts at the end and moves toward the begnning.

Method Detail

hasNext

public boolean hasNext(int windowSize,
              int increment)

Check if next window of specified size is available.

Parameters:

windowSize - Size of window. May be smaller or larger than default window size.

increment - The increment by which to move the window at each iteration. Note that this method does not actually change the position. However, it checks the sign of the increment parameter to determine the direction of the iteration.

Returns:

True if window of specified size is available.

Throws:

IllegalArgumentException - Window size parameter was not positive.

hasNext

public boolean hasNext()

Check if next window of default size is available.

Specified by:

hasNext in interface Iterator<Location>

Returns:

True if window of default size is available. The default size is the size specified in the LocIterator constructor.

remainder

public Location remainder()

Get portion of bounding location that has not yet been retrieved by next() method.

Returns:

The location not yet retrieved.

next

public Location next()

Get next window of default size, then increment position by default amount. Both defaults are specified in the LocIterator constructor.

Specified by:

next in interface Iterator<Location>

Returns:

Location of next window.

Throws:

IndexOutOfBoundsException - The next window was not within the bounding location.

next

public Location next(int windowSize,
            int increment)

Get next window of specified size, then increment position by specified amount.

Parameters:

windowSize - Size of window to get.

increment - Amount by which to shift position. If increment is positive, the position is shifted toward the end of the bounding location; if increment is negative, the position is shifted toward the beginning of the bounding location.

Returns:

Location of next window.

Throws:

IndexOutOfBoundsException - The next window was not within the bounding location.

IllegalArgumentException - The increment was zero, or windowSize was not positive.

toString

public String toString()

Get string representation of iterator.

Overrides:

toString in class Object

Returns:

Description of internal state.

remove

public void remove()

Unsupported.

Specified by:

remove in interface Iterator<Location>

Throws:

UnsupportedOperationException

main

@Deprecated
public static void main(String[] args)

Deprecated.