Package org.biojava.bio.seq
Class MergeFeatureHolder
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
org.biojava.bio.seq.MergeFeatureHolder
- All Implemented Interfaces:
Serializable
,FeatureHolder
,Changeable
FeatureHolder which exposes all the features in a set
of sub-FeatureHolders. This is provided primarily as
a support class for ViewSequence. It may also be useful
for other applications, such as simple distributed
annotation systems.
- Author:
- Thomas Down, Matthew Pocock
- See Also:
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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 TypeMethodDescriptionvoid
Add an extra FeatureHolder to the set of FeatureHolders which are merged.boolean
Check if the feature is present in this holder.int
Count how many features are contained.features()
Iterate over all the features in all child FeatureHolders.filter
(FeatureFilter ff, boolean recurse) When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.Return a schema-filter for thisFeatureHolder
.void
Remove a FeatureHolder from the set of FeatureHolders which are merged.Methods inherited from class org.biojava.bio.seq.AbstractFeatureHolder
createFeature, filter, removeFeature
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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MergeFeatureHolder
public MergeFeatureHolder()Create a new, empty, MergeFeatureHolder.
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Method Details
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addFeatureHolder
Add an extra FeatureHolder to the set of FeatureHolders which are merged. This method is provided for backward compatibility, and is equivalent to:mfh.addFeatureHolder(fh, FeatureFilter.all);
You should always use the two-arg version in preference if you are able to define the membership of a FeatureHolder.
- Throws:
ChangeVetoException
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removeFeatureHolder
Remove a FeatureHolder from the set of FeatureHolders which are merged.- Throws:
ChangeVetoException
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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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features
Iterate over all the features in all child FeatureHolders. The Iterator may throw ConcurrantModificationException if there is a change in the underlying collections during iteration.- Specified by:
features
in interfaceFeatureHolder
- Returns:
- an Iterator
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filter
When applied to a MergeFeatureHolder, this filters each child FeatureHolder independently.- 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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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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