Package org.biojava.bio.symbol

Class FuzzyLocation

java.lang.Object

org.biojava.bio.symbol.AbstractLocation

org.biojava.bio.symbol.AbstractRangeLocation

org.biojava.bio.symbol.FuzzyLocation

All Implemented Interfaces:

Serializable, Location

public class FuzzyLocation
extends AbstractRangeLocation
implements Serializable

A 'fuzzy' location a-la Embl fuzzy locations.

Fuzzy locations have propreties that indicate that they may start before min and end after max. However, this in no way affects how they interact with other locations.

Author:

Matthew Pocock, Thomas Down, Greg Cox

See Also:

Serialized Form

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field	Description
static FuzzyLocation.RangeResolver	RESOLVE_AVERAGE	Use the arithmetic mean of the `inner' and `outer' values, unless the outer value is unbounded.
static FuzzyLocation.RangeResolver	RESOLVE_INNER	Always use the `inner' values.
static FuzzyLocation.RangeResolver	RESOLVE_OUTER	Use the `outer' values, unless they are unbounded in which case the `inner' values are used.

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

empty, full, naturalOrder

Constructor Summary

Constructors

Constructor	Description
FuzzyLocation(int outerMin, int outerMax, int innerMin, int innerMax, boolean isMinFuzzy, boolean isMaxFuzzy, FuzzyLocation.RangeResolver resolver)	Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).
FuzzyLocation(int outerMin, int outerMax, int innerMin, int innerMax, FuzzyLocation.RangeResolver resolver)	Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).

Method Summary

Modifier and Type	Method	Description
int	getInnerMax()
int	getInnerMin()
int	getMax()	The maximum position contained.
int	getMin()	The minimum position contained.
int	getOuterMax()
int	getOuterMin()
FuzzyLocation.RangeResolver	getResolver()	Retrieve the Location that this decorates.
boolean	hasBoundedMax()
boolean	hasBoundedMin()
protected void	initializeVariables(int outerMin, int outerMax, int innerMin, int innerMax, boolean isMinFuzzy, boolean isMaxFuzzy, FuzzyLocation.RangeResolver resolver)	Refactored initialization code from the constructors.
boolean	isMaxFuzzy()
boolean	isMinFuzzy()
String	toString()
Location	translate(int dist)	Create a location that is a translation of this location.

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

Field Detail

RESOLVE_INNER

public static final FuzzyLocation.RangeResolver RESOLVE_INNER

Always use the `inner' values.

RESOLVE_OUTER

public static final FuzzyLocation.RangeResolver RESOLVE_OUTER

Use the `outer' values, unless they are unbounded in which case the `inner' values are used.

RESOLVE_AVERAGE

public static final FuzzyLocation.RangeResolver RESOLVE_AVERAGE

Use the arithmetic mean of the `inner' and `outer' values, unless the outer value is unbounded.

Constructor Detail

FuzzyLocation

public FuzzyLocation(int outerMin,
                     int outerMax,
                     int innerMin,
                     int innerMax,
                     FuzzyLocation.RangeResolver resolver)

Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax).

Parameters:

outerMin - the lower bound on the location's min value. Integer.MIN_VALUE indicates unbounded.

outerMax - the upper bound on the location's max value. Integer.MAX_VALUE indicates unbounded.

innerMin - the upper bound on the location's min value.

innerMax - the lower bound on the location's max value.

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

FuzzyLocation

public FuzzyLocation(int outerMin,
                     int outerMax,
                     int innerMin,
                     int innerMax,
                     boolean isMinFuzzy,
                     boolean isMaxFuzzy,
                     FuzzyLocation.RangeResolver resolver)

Create a new FuzzyLocation with endpoints (outerMin.innerMin) and (innerMax.outerMax). This constructor allows you to explicitly mark an endpoint as fuzzy, even if there is no other information about it. For example, a valid swissprot location "?5 10" would be a fuzzy location 5 to 10 where the min is fuzzy and the max is not.

Note that it is not logical to specify inner and outer values that clearly denote fuzzy boundaries and the set the isMinFuzzy or isMaxFuzzy value to false. This object makes no specific check of your logic so be careful.

Parameters:

outerMin - the lower bound on the location's min value. Integer.MIN_VALUE indicates unbounded.

outerMax - the upper bound on the location's max value. Integer.MAX_VALUE indicates unbounded.

innerMin - the upper bound on the location's min value.

innerMax - the lower bound on the location's max value.

isMinFuzzy - Explictly state if the minimum is fuzzy

isMaxFuzzy - Explictly state if the maximum is fuzzy

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

Method Detail

translate

public Location translate(int dist)

Description copied from interface: Location

Create a location that is a translation of this location.

Specified by:

translate in interface Location

Parameters:

dist - the distance to translate (to the right)

getResolver

public FuzzyLocation.RangeResolver getResolver()

Retrieve the Location that this decorates.

Returns:

the Location instance that stores all of the Location interface data

getOuterMin

public int getOuterMin()

getOuterMax

public int getOuterMax()

getInnerMin

public int getInnerMin()

getInnerMax

public int getInnerMax()

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

Specified by:

getMin in interface 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

Specified by:

getMax in interface Location

Returns:

the maximum position contained

hasBoundedMin

public boolean hasBoundedMin()

hasBoundedMax

public boolean hasBoundedMax()

toString

public String toString()

Overrides:

toString in class Object

isMinFuzzy

public boolean isMinFuzzy()

isMaxFuzzy

public boolean isMaxFuzzy()

initializeVariables

protected void initializeVariables(int outerMin,
                                   int outerMax,
                                   int innerMin,
                                   int innerMax,
                                   boolean isMinFuzzy,
                                   boolean isMaxFuzzy,
                                   FuzzyLocation.RangeResolver resolver)

Refactored initialization code from the constructors.

Parameters:

outerMin - the lower bound on the location's min value. Integer.MIN_VALUE indicates unbounded.

outerMax - the upper bound on the location's max value. Integer.MAX_VALUE indicates unbounded.

innerMin - the upper bound on the location's min value.

innerMax - the lower bound on the location's max value.

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