org.biojava.bio.symbol

Class FuzzyPointLocation

java.lang.Object

org.biojava.bio.symbol.AbstractLocation

org.biojava.bio.symbol.FuzzyPointLocation

All Implemented Interfaces:

Serializable, Location

public class FuzzyPointLocation
extends AbstractLocation

FuzzyPointLocation represents two types of EMBL-style partially-defined locations. These are the '(123.567)' type, which represent a single residue somewhere between these coordinates and the '<123' or '>123' type, which represent an unbounded location, not including the residue at that coordinate.

Author:

Keith James, Greg Cox

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	FuzzyPointLocation.PointResolver Determines how a FuzzyPointLocation should be treated when used as a normal Location.

Field Summary

Fields

Modifier and Type	Field and Description
static FuzzyPointLocation.PointResolver	RESOLVE_AVERAGE
static FuzzyPointLocation.PointResolver	RESOLVE_MAX
static FuzzyPointLocation.PointResolver	RESOLVE_MIN

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

empty, full, naturalOrder

Constructor Summary

Constructors

Constructor and Description
FuzzyPointLocation(int min, int max, FuzzyPointLocation.PointResolver resolver) Creates a new FuzzyPointLocation object.

Method Summary

Methods

Modifier and Type	Method and Description
Iterator	blockIterator() Return an Iterator over the set of maximal contiguous sub-locations.
boolean	contains(int point) Checks if this location contains a point.
boolean	contains(Location loc) Checks if this location contains the other.
boolean	equals(Location loc)
int	getMax() The maximum position contained.
int	getMin() The minimum position contained.
FuzzyPointLocation.PointResolver	getResolver()
boolean	hasBoundedMax()
boolean	hasBoundedMin()
int	hashCode()
Location	intersection(Location loc) Returns a Location that contains all points common to both ranges.
boolean	isContiguous() Determine if a Location is contiguous.
boolean	overlaps(Location loc) Checks if these two locations overlap, using this location's concept of overlapping.
SymbolList	symbols(SymbolList slist) Return the symbols in a sequence that fall within this range.
String	toString()
Location	translate(int dist) Create a location that is a translation of this location.

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

equals, getDecorator, newInstance, union

Methods inherited from class java.lang.Object

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

Field Detail

RESOLVE_MIN

public static final FuzzyPointLocation.PointResolver RESOLVE_MIN

RESOLVE_MAX

public static final FuzzyPointLocation.PointResolver RESOLVE_MAX

RESOLVE_AVERAGE

public static final FuzzyPointLocation.PointResolver RESOLVE_AVERAGE

Constructor Detail

FuzzyPointLocation

public FuzzyPointLocation(int min,
                  int max,
                  FuzzyPointLocation.PointResolver resolver)

Creates a new FuzzyPointLocation object. If the minimum value is equal to the maximum value, it is interperted as a swissprot point location such as "?24". If the minimum is Integer.MIN_VALUE and the maximum is Integer.MAX_VALUE, it is interperted as a swissprot location like '?'.

Parameters:

min - an int value for the minimum boundary of the location, Integer.MIN_VALUE if unbounded.

max - an int value for the minimum boundary of the location, Integer.MAX_VALUE if unbounded.

resolver - a PointResolver which defines the policy used to calculate the location's min and max properties.

Method Detail

getResolver

public FuzzyPointLocation.PointResolver getResolver()

getMin

public int getMin()

Description copied from interface: Location

The minimum position contained.

WARNING: The location will not contain every point between getMin() and getMax() if isContiguous() is false. If isContiguous() does return false you should use the Iterator returned by blockIterator() to iterate over the minimum set of contiguous blocks that make up this Location

Returns:

the minimum position contained

getMax

public int getMax()

Description copied from interface: Location

The maximum position contained.

WARNING: The location will not contain every point between getMin() and getMax() if isContiguous() is false. If isContiguous() does return false you should use the Iterator returned by blockIterator() to iterate over the minimum set of contiguous blocks that make up this Location

Returns:

the maximum position contained

hasBoundedMin

public boolean hasBoundedMin()

hasBoundedMax

public boolean hasBoundedMax()

overlaps

public boolean overlaps(Location loc)

Description copied from interface: Location

Checks if these two locations overlap, using this location's concept of overlapping.

Abstractly, two locations overlap if they both contain any point.

Specified by:

overlaps in interface Location

Overrides:

overlaps in class AbstractLocation

Parameters:

loc - the Location to check

Returns:

true if they overlap, otherwise false

contains

public boolean contains(Location loc)

Description copied from interface: Location

Checks if this location contains the other.

Abstractly, a location contains another if every point in the other location is contained within this one.

Specified by:

contains in interface Location

Overrides:

contains in class AbstractLocation

Parameters:

loc - the Location to check

Returns:

true if this contains l, otherwise false

contains

public boolean contains(int point)

Description copied from interface: Location

Checks if this location contains a point.

Parameters:

point - the point to check

Returns:

true if this contains p, otherwise false

equals

public boolean equals(Location loc)

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractLocation

intersection

public Location intersection(Location loc)

Description copied from interface: Location

Returns a Location that contains all points common to both ranges.

Specified by:

intersection in interface Location

Overrides:

intersection in class AbstractLocation

Parameters:

loc - the Location to intersect with

Returns:

a Location containing all points common to both, or the empty range if there are no such points

symbols

public SymbolList symbols(SymbolList slist)

Description copied from interface: Location

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

Parameters:

slist - the SymbolList to process

Returns:

the SymbolList containing the symbols in seq in this range

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.

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

translate

public Location translate(int dist)

Description copied from interface: Location

Create a location that is a translation of this location.

Parameters:

dist - the distance to translate (to the right)

toString

public String toString()

Overrides:

toString in class Object