org.biojava.bio.seq.projection
Class ProjectedFeature

java.lang.Object
  extended byorg.biojava.bio.seq.projection.ProjectedFeature
All Implemented Interfaces:
Annotatable, Changeable, Feature, FeatureHolder, Projection
Direct Known Subclasses:
ProjectedStrandedFeature

public class ProjectedFeature
extends java.lang.Object
implements Feature, Projection

Internal class used by ProjectionEngine to wrap Feature objects.

Since:
1.1
Author:
Thomas Down

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.seq.Feature
Feature.ByLocationComparator, Feature.Template
 
Nested classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, TYPE
 
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
 
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
 
Constructor Summary
ProjectedFeature(Feature f, ProjectionContext ctx)
           
 
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.
 boolean equals(java.lang.Object o)
           
 java.util.Iterator features()
          Iterate over any child features which are held by this feature.
 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.
 Annotation getAnnotation()
          Should return the associated annotation object.
 Location getLocation()
          The location of this feature.
 FeatureHolder getParent()
          Return the FeatureHolder to which this feature has been attached.
protected  FeatureHolder getProjectedFeatures()
           
 ProjectionContext getProjectionContext()
           
 FeatureFilter getSchema()
          Return a schema-filter for this FeatureHolder.
 Sequence getSequence()
          Return the Sequence object to which this feature is (ultimately) attached.
 java.lang.String getSource()
          The source of the feature.
 SymbolList getSymbols()
          Return a list of symbols that are contained in this feature.
 java.lang.String getType()
          The type of the feature.
 Feature getViewedFeature()
           
 int hashCode()
           
 boolean isUnchanging(ChangeType ct)
           A particular ChangeType can never be raised by this Changeable.
 Feature.Template makeTemplate()
          Create a new Template that could be used to generate a feature identical to this one.
 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.
 void setLocation(Location loc)
          The new location for this feature.
 void setSource(java.lang.String source)
          Change the source of the Feature.
 void setType(java.lang.String type)
          Change the type of this feature.
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProjectedFeature

public ProjectedFeature(Feature f,
                        ProjectionContext ctx)
Method Detail

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

getViewedFeature

public Feature getViewedFeature()
Specified by:
getViewedFeature in interface Projection

getProjectionContext

public ProjectionContext getProjectionContext()
Specified by:
getProjectionContext in interface Projection

makeTemplate

public Feature.Template makeTemplate()
Description copied from interface: Feature
Create a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.

Specified by:
makeTemplate in interface Feature
Returns:
a new Template that would make a feature like this one

getLocation

public Location getLocation()
Description copied from interface: Feature
The location of this feature.

The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.

Specified by:
getLocation in interface Feature
Returns:
a Location anchoring this feature

setLocation

public void setLocation(Location loc)
                 throws ChangeVetoException
Description copied from interface: Feature
The new location for this feature.

The location may be complicated or simply a range. The annotation is assumed to apply to the entire region contained within the location. Any values returned from methods that rely on the old location must not be affected.

Specified by:
setLocation in interface Feature
Parameters:
loc - the new Location for this feature
Throws:
ChangeVetoException - if the location can't be altered

getParent

public FeatureHolder getParent()
Description copied from interface: Feature
Return the FeatureHolder to which this feature has been attached. This will be a Sequence object for top level features, and a Feature object for features further down the tree.

Specified by:
getParent in interface Feature

getSequence

public Sequence getSequence()
Description copied from interface: Feature
Return the Sequence object to which this feature is (ultimately) attached. For top level features, this will be equal to the FeatureHolder returned by getParent.

Specified by:
getSequence in interface Feature
Returns:
the ultimate parent Sequence

getType

public java.lang.String getType()
Description copied from interface: Feature
The type of the feature.

Specified by:
getType in interface Feature
Returns:
the type of this sequence

setType

public void setType(java.lang.String type)
             throws ChangeVetoException
Description copied from interface: Feature
Change the type of this feature.

Specified by:
setType in interface Feature
Throws:
ChangeVetoException - if the type can't be altered

getSource

public java.lang.String getSource()
Description copied from interface: Feature
The source of the feature. This may be a program or process.

Specified by:
getSource in interface Feature
Returns:
the source, or generator

setSource

public void setSource(java.lang.String source)
               throws ChangeVetoException
Description copied from interface: Feature
Change the source of the Feature.

Specified by:
setSource in interface Feature
Parameters:
source - the new source String
Throws:
ChangeVetoException - if the source can't be altered

getAnnotation

public Annotation getAnnotation()
Description copied from interface: Annotatable
Should return the associated annotation object.

Specified by:
getAnnotation in interface Annotatable
Returns:
an Annotation object, never null

getSymbols

public SymbolList getSymbols()
Description copied from interface: Feature
Return a list of symbols that are contained in this feature.

The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

If the feature location is modified then this does not modify any SymbolList produced by earlier invocations of this method.

Specified by:
getSymbols in interface Feature
Returns:
a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

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

getProjectedFeatures

protected FeatureHolder getProjectedFeatures()

features

public java.util.Iterator features()
Description copied from interface: Feature
Iterate over any child features which are held by this feature. The order of iteration MAY be significant for some types of Feature.

Specified by:
features in interface Feature

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,
                             BioException
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
BioException - if something went wrong during creating the feature

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

hashCode

public int hashCode()

equals

public boolean equals(java.lang.Object o)

addChangeListener

public 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

removeChangeListener

public 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

addChangeListener

public 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 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