java.lang.Object
- 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.
When implementing a new Location decorator.

Author:

Matthew Pocock

Field Summary
- Fields inherited from interface org.biojava.bio.symbol.Location
  empty, full, naturalOrder

Constructor Summary

Constructors
Modifier Constructor Description

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

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
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`	`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

Class AbstractLocationDecorator

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AbstractLocationDecorator

Method Detail

getWrapped

decorate

newInstance

getDecorator

getMin

getMax

overlaps

contains

contains

equals

intersection

union

symbols

translate

isContiguous

blockIterator