Class ProjectedFeature
- All Implemented Interfaces:
Annotatable
,Feature
,FeatureHolder
,Projection
,Changeable
- Since:
- 1.1
- Author:
- Thomas Down, Matthew Pocock
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparator, Feature.Template
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.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM
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 a listener that will be informed of all changes.void
Add a listener that will be informed of changes of a given type.boolean
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.boolean
features()
Iterate over any child features which are held by this feature.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.Return theFeatureHolder
to which this feature has been attached.protected FeatureHolder
Return theSequence
object to which this feature is (ultimately) attached.Return a list of symbols that are contained in this feature.int
hashCode()
boolean
A particular ChangeType can never be raised by this Changeable.Create a new Template that could be used to generate a feature identical to this one.void
Remove a listener that was interested in all types of changes.void
Remove a listener that was interested in a specific types of changes.void
Remove a feature from this FeatureHolder.Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.bio.seq.Feature
getLocation, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTerm
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
getSchema
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Constructor Details
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ProjectedFeature
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Method Details
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getViewedFeature
- Specified by:
getViewedFeature
in interfaceProjection
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getProjectionContext
- Specified by:
getProjectionContext
in interfaceProjection
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getSequence
Description copied from interface:Feature
Return theSequence
object to which this feature is (ultimately) attached. For top level features, this will be equal to theFeatureHolder
returned bygetParent
.- Specified by:
getSequence
in interfaceFeature
- Returns:
- the ultimate parent Sequence
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getParent
Description copied from interface:Feature
Return theFeatureHolder
to which this feature has been attached. This will be aSequence
object for top level features, and aFeature
object for features further down the tree. -
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 interfaceFeature
- Returns:
- a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent
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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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getProjectedFeatures
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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 interfaceFeature
- Specified by:
features
in interfaceFeatureHolder
- Returns:
- an Iterator
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filter
Description copied from interface:FeatureHolder
Query this set of features using a suppliedFeatureFilter
.- Specified by:
filter
in interfaceFeatureHolder
- 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
- 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
- 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
- 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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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 interfaceFeature
- Returns:
- a new Template that would make a feature like this one
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hashCode
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equals
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addChangeListener
Description copied from interface:Changeable
Add a listener that will be informed of all changes.- Specified by:
addChangeListener
in interfaceChangeable
- Parameters:
cl
- the ChangeListener to add
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removeChangeListener
Description copied from interface:Changeable
Remove a listener that was interested in all types of changes.- Specified by:
removeChangeListener
in interfaceChangeable
- Parameters:
cl
- a ChangeListener to remove
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addChangeListener
Description copied from interface:Changeable
Add a listener that will be informed of changes of a given type.- Specified by:
addChangeListener
in interfaceChangeable
- Parameters:
cl
- the ChangeListenerct
- the ChangeType it is to be informed of
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removeChangeListener
Description copied from interface:Changeable
Remove a listener that was interested in a specific types of changes.- Specified by:
removeChangeListener
in interfaceChangeable
- Parameters:
cl
- a ChangeListener to removect
- the ChangeType that it was interested in
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isUnchanging
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 interfaceChangeable
- Parameters:
ct
- the ChangeType to check- Returns:
- true if ChangeEvents of this type are guaranteed to never be fired
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