Package org.biojava.bio.seq.projection
Class ProjectedFeatureHolder
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
org.biojava.bio.seq.projection.ProjectedFeatureHolder
- All Implemented Interfaces:
Serializable
,FeatureHolder
,Changeable
public final class ProjectedFeatureHolder
extends AbstractFeatureHolder
implements FeatureHolder, Serializable
Helper class for projecting Feature objects into an alternative
coordinate system. This class offers a view onto a set of features,
projecting them into a different coordinate system, and also changing
their
parent
property. The destination coordinate system
can run in the opposite direction from the source, in which case the
strand
property of StrandedFeatures is flipped.
The projected features returned by this class are small proxy objects.
Proxy classes are autogenerated on demand for any sub-interface of
Feature
by the ProjectionEngine
class.
- Since:
- 1.1
- Author:
- Thomas Down, Matthew Pocock
- See Also:
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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Field Summary
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
Check if the feature is present in this holder.int
Count how many features are contained.createFeature
(Feature.Template templ) Create a new Feature, and add it to this FeatureHolder.features()
Iterate over the features in no well defined order.filter
(FeatureFilter ff) Query this set of features using a suppliedFeatureFilter
.filter
(FeatureFilter ff, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.protected ChangeEvent
Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolderReturn a schema-filter for thisFeatureHolder
.protected FeatureHolder
Called internally to construct a lightweight projected view of a set of featuresvoid
removeFeature
(Feature dyingChild) Remove a feature from this FeatureHolder.Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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ProjectedFeatureHolder
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Method Details
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getContext
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features
Description copied from interface:FeatureHolder
Iterate over the features in no well defined order.- Specified by:
features
in interfaceFeatureHolder
- Returns:
- an Iterator
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countFeatures
Description copied from interface:FeatureHolder
Count how many features are contained.- Specified by:
countFeatures
in interfaceFeatureHolder
- Returns:
- a positive integer or zero, equal to the number of features contained
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containsFeature
Description copied from interface:FeatureHolder
Check if the feature is present in this holder.- Specified by:
containsFeature
in interfaceFeatureHolder
- Parameters:
f
- the Feature to check- Returns:
- true if f is in this set
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filter
Description copied from interface:FeatureHolder
Query this set of features using a suppliedFeatureFilter
.- Specified by:
filter
in interfaceFeatureHolder
- Overrides:
filter
in classAbstractFeatureHolder
- Parameters:
ff
- theFeatureFilter
to apply.- Returns:
- all features in this container which match
filter
.
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filter
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 interfaceFeatureHolder
- Overrides:
filter
in classAbstractFeatureHolder
- Parameters:
ff
- the FeatureFilter to applyrecurse
- 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.
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createFeature
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 interfaceFeatureHolder
- Overrides:
createFeature
in classAbstractFeatureHolder
- Throws:
ChangeVetoException
- if this FeatureHolder does not support creation of new features, or if the change was vetoedBioException
- if something went wrong during creating the feature
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removeFeature
Description copied from interface:FeatureHolder
Remove a feature from this FeatureHolder.- Specified by:
removeFeature
in interfaceFeatureHolder
- Overrides:
removeFeature
in classAbstractFeatureHolder
- Throws:
ChangeVetoException
- if this FeatureHolder does not support feature removal or if the change was vetoedBioException
- if there was an error removing the feature
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getSchema
Description copied from interface:FeatureHolder
Return a schema-filter for thisFeatureHolder
. This is a filter which allFeature
s immediately contained by thisFeatureHolder
will match. It need not directly match their child features, but it can (and should!) provide information about them usingFeatureFilter.OnlyChildren
filters. In cases where there is no feature hierarchy, this can be indicated by includingFeatureFilter.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, returnFeatureFilter.top_level
.Feature
objects should, as a minimum, returnFeatureFilter.ByParent(new FeatureFilter.ByFeature(this))
.- Specified by:
getSchema
in interfaceFeatureHolder
- Returns:
- the schema filter
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makeProjectionSet
Called internally to construct a lightweight projected view of a set of features -
forwardChangeEvent
Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder
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