org.biojava.bio.symbol

Class MergeLocation

java.lang.Object

org.biojava.bio.symbol.AbstractLocation

org.biojava.bio.symbol.AbstractRangeLocation

org.biojava.bio.symbol.RangeLocation

org.biojava.bio.symbol.MergeLocation

All Implemented Interfaces:

Serializable, Location

public class MergeLocation
extends RangeLocation

Produced by LocationTools as a result of union operations. It's a RangeLocation and can be used as such but it also retains knowledge of which individual components made it up. None of the methods of RangeLocation are overridden only new methods have been added to get the subcomponents.

For example a union operation between the following locations [1,20],[27,45],[30-70] will produce a CompoundLocation like this: {[1,20],[27,70]}, the last two locations have been merged into a MergeLocation which contains the two subcomponents.

Copyright: Copyright (c) 2002

Company: AgResearch

Version:

1.0

Author:

Mark Schreiber, Francois Pepin

See Also:

Serialized Form

Field Summary

Fields inherited from interface org.biojava.bio.symbol.Location

empty, full, naturalOrder

Method Summary

Methods

Modifier and Type	Method and Description
ListIterator	componentLocationIterator()
List	getComponentList(boolean recurse) Gets the component locations that make up this one
static MergeLocation	mergeLocations(List componentLocations) Static Factory method for getting an instance of a MergeLocation
static MergeLocation	mergeLocations(Location locA, Location locB)

Methods inherited from class org.biojava.bio.symbol.RangeLocation

getMax, getMin, toString, translate

Methods inherited from class org.biojava.bio.symbol.AbstractRangeLocation

blockIterator, contains, isContiguous, symbols

Methods inherited from class org.biojava.bio.symbol.AbstractLocation

contains, equals, getDecorator, hashCode, intersection, newInstance, overlaps, union

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Method Detail

getComponentList

public List getComponentList(boolean recurse)

Gets the component locations that make up this one

Parameters:

recurse - if true the method lists the component locations of all nested MergedLocations.

Returns:

a List of Locations.

componentLocationIterator

public ListIterator componentLocationIterator()

Returns:

A ListIterator over the component locations. The iterator does not recurse nested MergeLocations.

mergeLocations

public static MergeLocation mergeLocations(List componentLocations)
                                    throws BioException

Static Factory method for getting an instance of a MergeLocation

Parameters:

componentLocations - the Locations to Merge

Returns:

the merged location

Throws:

BioException - if the list contains objects that are not Locations or if the locations don't represent a contiguous block. Use LocationTools.union() if you want to merge discontinuous blocks.

mergeLocations

public static MergeLocation mergeLocations(Location locA,
                           Location locB)
                                    throws BioException

Throws:

BioException