Package org.biojava.bio.symbol

Class AbstractRangeLocation

java.lang.Object

org.biojava.bio.symbol.AbstractLocation

org.biojava.bio.symbol.AbstractRangeLocation

All Implemented Interfaces:

Serializable, Location

Direct Known Subclasses:

FuzzyLocation, PointLocation, RangeLocation

public abstract class AbstractRangeLocation
extends AbstractLocation

Base class for simple contiguous Location implementations. Just implement getMin and getMax, and translate..

Author:

Matthew Pocock, Keith James

See Also:

Serialized Form

Field Summary

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

empty, full, naturalOrder

Constructor Summary

Constructors

Constructor	Description
AbstractRangeLocation()

Method Summary

Modifier and Type	Method	Description
Iterator	blockIterator()	Return an Iterator over the set of maximal contiguous sub-locations.
boolean	contains(int p)	Checks if this location contains a point.
boolean	isContiguous()	Determine if a Location is contiguous.
SymbolList	symbols(SymbolList seq)	Return the symbols in a sequence that fall within this range.

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, toString, wait, wait, wait

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

getMax, getMin, translate

Constructor Detail

AbstractRangeLocation

public AbstractRangeLocation()

Method Detail

blockIterator

public Iterator blockIterator()

Description copied from interface: Location

Return an Iterator over the set of maximal contiguous sub-locations.

Given any location, it can be considered to contain zero or more maximal contiguous blocks of width 1 or greater. The empty location is composed from nothing. A contiguous location is composed from itself. A non-contiguous location is composed from contiguous blocks seperated by gaps.

This method should return an Iterator over these maximally contiguous blocks starting with the left-most block, and finishing at the right-most block.

Returns:

an Iterator over Location objects that are the maximally contiguous set of locations contained within this location

isContiguous

public boolean isContiguous()

Description copied from interface: Location

Determine if a Location is contiguous.

Returns:

true if and only if this Location contains every point from min to max inclusive.

symbols

public SymbolList symbols(SymbolList seq)

Description copied from interface: Location

Return the symbols in a sequence that fall within this range.

Parameters:

seq - the SymbolList to process

Returns:

the SymbolList containing the symbols in seq in this range

contains

public boolean contains(int p)

Description copied from interface: Location

Checks if this location contains a point.

Parameters:

p - the point to check

Returns:

true if this contains p, otherwise false