Package org.biojava.bio.seq
Class FeatureHolder.EmptyFeatureHolder
java.lang.Object
org.biojava.utils.Unchangeable
org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
- All Implemented Interfaces:
FeatureHolder
,Changeable
- Enclosing interface:
FeatureHolder
public static final class FeatureHolder.EmptyFeatureHolder
extends Unchangeable
implements FeatureHolder
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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 TypeMethodDescriptionboolean
Check if the feature is present in this holder.int
Count how many features are contained.Create a new Feature, and add it to this FeatureHolder.features()
Iterate over the features in no well defined order.filter
(FeatureFilter fc) Query this set of features using a suppliedFeatureFilter
.filter
(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.Return a schema-filter for thisFeatureHolder
.void
Remove a feature from this FeatureHolder.Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
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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EmptyFeatureHolder
public EmptyFeatureHolder()
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Method Details
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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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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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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
- Parameters:
fc
- 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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filter
Description copied from interface:FeatureHolder
Query this set of features using a suppliedFeatureFilter
.- Specified by:
filter
in interfaceFeatureHolder
- Parameters:
fc
- theFeatureFilter
to apply.- Returns:
- all features in this container which match
filter
.
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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
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removeFeature
Description copied from interface:FeatureHolder
Remove a feature from this FeatureHolder.- Specified by:
removeFeature
in interfaceFeatureHolder
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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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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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