org.biojava.bio.seq.impl
Class LazyFilterFeatureHolder

java.lang.Object
  extended byorg.biojava.bio.seq.impl.LazyFilterFeatureHolder
All Implemented Interfaces:
Changeable, FeatureHolder

public class LazyFilterFeatureHolder
extends java.lang.Object
implements FeatureHolder

FeatureHolder which lazily applies a specified filter to another FeatureHolder. This means that when you use a second filter to query the LazyFilterFeatureHolder, the underlying holder receives a single filter request with the two queries ANDed together.

Since:
1.3
Author:
Thomas Down

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
 
Constructor Summary
LazyFilterFeatureHolder(FeatureHolder fh, FeatureFilter ff)
           
 
Method Summary
 void addChangeListener(ChangeListener cl)
          Add a listener that will be informed of all changes.
 void addChangeListener(ChangeListener cl, ChangeType ct)
          Add a listener that will be informed of changes of a given type.
 boolean containsFeature(Feature f)
          Check if the feature is present in this holder.
 int countFeatures()
          Count how many features are contained.
 Feature createFeature(Feature.Template temp)
          Create a new Feature, and add it to this FeatureHolder.
 java.util.Iterator features()
          Iterate over the features in no well defined order.
 FeatureHolder filter(FeatureFilter ff)
          Query this set of features using a supplied FeatureFilter.
 FeatureHolder filter(FeatureFilter ff, boolean recurse)
          Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
protected  ChangeSupport getChangeSupport()
           
 FeatureFilter getSchema()
          Return a schema-filter for this FeatureHolder.
protected  boolean hasListeners()
           
 boolean isUnchanging(ChangeType ct)
           A particular ChangeType can never be raised by this Changeable.
 void removeChangeListener(ChangeListener cl)
          Remove a listener that was interested in all types of changes.
 void removeChangeListener(ChangeListener cl, ChangeType ct)
          Remove a listener that was interested in a specific types of changes.
 void removeFeature(Feature f)
          Remove a feature from this FeatureHolder.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

LazyFilterFeatureHolder

public LazyFilterFeatureHolder(FeatureHolder fh,
                               FeatureFilter ff)
Method Detail

features

public java.util.Iterator features()
Description copied from interface: FeatureHolder
Iterate over the features in no well defined order.

Specified by:
features in interface FeatureHolder
Returns:
an Iterator

countFeatures

public int countFeatures()
Description copied from interface: FeatureHolder
Count how many features are contained.

Specified by:
countFeatures in interface FeatureHolder
Returns:
a positive integer or zero, equal to the number of features contained

containsFeature

public boolean containsFeature(Feature f)
Description copied from interface: FeatureHolder
Check if the feature is present in this holder.

Specified by:
containsFeature in interface FeatureHolder
Parameters:
f - the Feature to check
Returns:
true if f is in this set

filter

public FeatureHolder filter(FeatureFilter ff)
Description copied from interface: FeatureHolder
Query this set of features using a supplied FeatureFilter.

Specified by:
filter in interface FeatureHolder
Parameters:
ff - the FeatureFilter to apply.
Returns:
all features in this container which match filter.

filter

public FeatureHolder filter(FeatureFilter ff,
                            boolean recurse)
Description copied from interface: FeatureHolder
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

Specified by:
filter in interface FeatureHolder
Parameters:
ff - the FeatureFilter to apply
recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

createFeature

public Feature createFeature(Feature.Template temp)
                      throws ChangeVetoException
Description copied from interface: FeatureHolder
Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

Specified by:
createFeature in interface FeatureHolder
Throws:
ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException
Description copied from interface: FeatureHolder
Remove a feature from this FeatureHolder.

Specified by:
removeFeature in interface FeatureHolder
Throws:
ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed

hasListeners

protected boolean hasListeners()

getChangeSupport

protected ChangeSupport getChangeSupport()

addChangeListener

public final void addChangeListener(ChangeListener cl)
Description copied from interface: Changeable
Add a listener that will be informed of all changes.

Specified by:
addChangeListener in interface Changeable
Parameters:
cl - the ChangeListener to add

addChangeListener

public final void addChangeListener(ChangeListener cl,
                                    ChangeType ct)
Description copied from interface: Changeable
Add a listener that will be informed of changes of a given type.

Specified by:
addChangeListener in interface Changeable
Parameters:
cl - the ChangeListener
ct - the ChangeType it is to be informed of

removeChangeListener

public final void removeChangeListener(ChangeListener cl)
Description copied from interface: Changeable
Remove a listener that was interested in all types of changes.

Specified by:
removeChangeListener in interface Changeable
Parameters:
cl - a ChangeListener to remove

removeChangeListener

public final void removeChangeListener(ChangeListener cl,
                                       ChangeType ct)
Description copied from interface: Changeable
Remove a listener that was interested in a specific types of changes.

Specified by:
removeChangeListener in interface Changeable
Parameters:
cl - a ChangeListener to remove
ct - the ChangeType that it was interested in

isUnchanging

public boolean isUnchanging(ChangeType ct)
Description copied from interface: Changeable

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

Specified by:
isUnchanging in interface Changeable
Parameters:
ct - the ChangeType to check
Returns:
true if ChangeEvents of this type are guaranteed to never be fired

getSchema

public FeatureFilter getSchema()
Description copied from interface: FeatureHolder
Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

Specified by:
getSchema in interface FeatureHolder
Returns:
the schema filter