org.biojava.bio.symbol
Class AbstractLocationDecorator

java.lang.Object
  extended by org.biojava.bio.symbol.AbstractLocationDecorator
All Implemented Interfaces:
Location
Direct Known Subclasses:
BetweenLocation, CircularLocation

public abstract class AbstractLocationDecorator
extends Object
implements Location

Abstract Location decorator (wrapper).

These wrap up a normal Location object, and act as markers to indicate that the location has some kind of special semantics.

Author:
Matthew Pocock
For developers:
When implementing a new Location decorator.

Field Summary
 
Fields inherited from interface org.biojava.bio.symbol.Location
empty, full, naturalOrder
 
Constructor Summary
protected AbstractLocationDecorator(Location wrapped)
          Construct a new decorator wrapping the specified Location.
 
Method Summary
 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 contains(Location l)
          Checks if this location contains the other.
protected abstract  Location decorate(Location loc)
           
 boolean equals(Object o)
          Checks if this location is equivalent to the other.
 Location getDecorator(Class decoratorClass)
          Checks the decorator chain for an instance of decoratorClass and return it if found.
 int getMax()
          The maximum position contained.
 int getMin()
          The minimum position contained.
protected  Location getWrapped()
           
 Location intersection(Location l)
          Returns a Location that contains all points common to both ranges.
 boolean isContiguous()
          Determine if a Location is contiguous.
 Location newInstance(Location loc)
          Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
 boolean overlaps(Location l)
          Checks if these two locations overlap, using this location's concept of overlapping.
 SymbolList symbols(SymbolList seq)
          Return the symbols in a sequence that fall within this range.
 Location translate(int dist)
          Create a location that is a translation of this location.
 Location union(Location l)
          Return a Location containing all points in either ranges.
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AbstractLocationDecorator

protected AbstractLocationDecorator(Location wrapped)
Construct a new decorator wrapping the specified Location.

Method Detail

getWrapped

protected final Location getWrapped()

decorate

protected abstract Location decorate(Location loc)

newInstance

public Location newInstance(Location loc)
Description copied from interface: Location
Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.

The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates loc.

Specified by:
newInstance in interface Location
Parameters:
loc - the Location to use as template
Returns:
a Location instance based on loc with the same decorators as the current instance

getDecorator

public Location getDecorator(Class decoratorClass)
Description copied from interface: Location
Checks the decorator chain for an instance of decoratorClass and return it if found.

The default behavior is to return null. If the current object is a decorator and is an instance of decoratorClass it should return itself. Otherwise, the decorator should chain this method onto the instance it wraps.

Specified by:
getDecorator in interface Location
Parameters:
decoratorClass - the Class to check
Returns:
a Location if an instance of this class is present in the decorator chain and null otherwise.

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

overlaps

public boolean overlaps(Location l)
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
Parameters:
l - the Location to check
Returns:
true if they overlap, otherwise false

contains

public boolean contains(Location l)
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
Parameters:
l - the Location to check
Returns:
true if this contains l, otherwise false

contains

public boolean contains(int p)
Description copied from interface: Location
Checks if this location contains a point.

Specified by:
contains in interface Location
Parameters:
p - the point to check
Returns:
true if this contains p, otherwise false

equals

public boolean equals(Object o)
Description copied from interface: Location
Checks if this location is equivalent to the other.

Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) && b.contains(a). You should call LocationTools.areEqual after casting l to Location.

Specified by:
equals in interface Location
Overrides:
equals in class Object
Parameters:
o - the Object to check
Returns:
true if this equals l, otherwise false

intersection

public Location intersection(Location l)
Description copied from interface: Location
Returns a Location that contains all points common to both ranges.

Specified by:
intersection in interface Location
Parameters:
l - the Location to intersect with
Returns:
a Location containing all points common to both, or the empty range if there are no such points

union

public Location union(Location l)
Description copied from interface: Location
Return a Location containing all points in either ranges.

Specified by:
union in interface Location
Parameters:
l - the Location to union with
Returns:
a Location representing the union

symbols

public SymbolList symbols(SymbolList seq)
Description copied from interface: Location
Return the symbols in a sequence that fall within this range.

Specified by:
symbols in interface Location
Parameters:
seq - the SymbolList to process
Returns:
the SymbolList containing the symbols in seq in this range

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)

isContiguous

public boolean isContiguous()
Description copied from interface: Location
Determine if a Location is contiguous.

Specified by:
isContiguous in interface Location
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.

Specified by:
blockIterator in interface Location
Returns:
an Iterator over Location objects that are the maximally contiguous set of locations contained within this location