org.biojava.bio.symbol
Interface Location

All Known Implementing Classes:
AbstractLocation, AbstractLocationDecorator, PointLocation

public interface Location

A set of integers, often used to represent positions on biological sequences.

The location will contain some indices between getMin and getMax inclusive. It is not required to contain all indices within this range. It is meant to contain the indices returned by the getMin or getMax. In the event that an operation would produce an invalid or nonsensical range, Location.empty should be returned.

Location objects are always immutable.

Working with locations

Locations can be constructed in a number of ways:

 Location l1 = LocationTools.makeLocation(10, 20);  // Makes a RangeLocation
 Location l2 = LocationTools.makeLocation(25, 25);  // Makes a PointLocation
 Location l3 = LocationTools.union(l1, l2); // Construct a non-contiguous
                                            // location containing the
                                            // points from l1 and l2
 

Author:
Matthew Pocock, Thomas Down

Field Summary
static Location empty
          The Location which contains no points.
static org.biojava.bio.symbol.LocationComparator naturalOrder
          Comparator which orders Locations naturally.
 
Method Summary
 java.util.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.
 boolean equals(java.lang.Object l)
          Checks if this location is equivalent to the other.
 Location getDecorator(java.lang.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.
 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.
 

Field Detail

empty

public static final Location empty
The Location which contains no points.

This object contains nothing. Its minimum value is Integer.MAX_VALUE. Its maximum value is Integer.MIN_VALUE. It overlaps nothing. It is equal to nothing. Intersection results in the empty range. Union results in the argument range. Symbols returns an empty array.

Every day, in every way, empty becomes more and more boring.


naturalOrder

public static final org.biojava.bio.symbol.LocationComparator naturalOrder
Comparator which orders Locations naturally. Locations are sorted primarily on the basis of their getMin() value. In cases where that is equal, they are secondarily sorted by getMax() value.

Method Detail

newInstance

public 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.

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.

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(java.lang.Class decoratorClass)
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.

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()
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()
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

overlaps

public boolean overlaps(Location l)
Checks if these two locations overlap, using this location's concept of overlapping.

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

Parameters:
l - the Location to check
Returns:
true if they overlap, otherwise false

contains

public boolean contains(Location l)
Checks if this location contains the other.

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

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

contains

public boolean contains(int p)
Checks if this location contains a point.

Parameters:
p - the point to check
Returns:
true if this contains p, otherwise false

equals

public boolean equals(java.lang.Object l)
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.

Parameters:
l - the Object to check
Returns:
true if this equals l, otherwise false

intersection

public Location intersection(Location l)
Returns a Location that contains all points common to both ranges.

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)
Return a Location containing all points in either ranges.

Parameters:
l - the Location to union with
Returns:
a Location representing the union

symbols

public SymbolList symbols(SymbolList seq)
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

translate

public Location translate(int dist)
Create a location that is a translation of this location.

Parameters:
dist - the distance to translate (to the right)

isContiguous

public boolean isContiguous()
Determine if a Location is contiguous.

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

blockIterator

public java.util.Iterator blockIterator()
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