org.biojava.bio.seq.projection
Class ProjectedFeature

java.lang.Object
  |
  +--org.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

Returns:

an Iterator

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()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

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