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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleFeature
public class SimpleFeature
A no-frills implementation of a feature.
SimpleRichFeature
,
Serialized FormNested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature |
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Feature.ByLocationComparator, Feature.Template |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
---|
FeatureHolder.EmptyFeatureHolder |
Field Summary |
---|
Fields inherited from interface org.biojava.bio.seq.Feature |
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byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
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EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Constructor Summary | |
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SimpleFeature(Sequence sourceSeq,
FeatureHolder parent,
Feature.Template template)
Create a SimpleFeature on the given sequence. |
Method Summary | |
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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)
|
protected boolean |
featureHolderAllocated()
A utility function to find out if the feature holder delegate has been instantiated yet. |
java.util.Iterator |
features()
Iterate over any child features which are held by this feature. |
protected void |
fillTemplate(Feature.Template ft)
|
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. |
protected ChangeSupport |
getChangeSupport(ChangeType ct)
Called to retrieve the ChangeSupport for this object. |
protected SimpleFeatureHolder |
getFeatureHolder()
A utility function to retrieve the feature holder delegate, creating it if necessary. |
Location |
getLocation()
The location of this feature. |
FeatureHolder |
getParent()
Return the FeatureHolder to which this feature has been
attached. |
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. |
Term |
getSourceTerm()
An ontology term defining the source of this feature. |
SymbolList |
getSymbols()
Return a list of symbols that are contained in this feature. |
java.lang.String |
getType()
The type of the feature. |
Term |
getTypeTerm()
An ontology term defining the type of feature. |
int |
hashCode()
|
Feature.Template |
makeTemplate()
Create a new Template that could be used to generate a feature identical to this one. |
Feature |
realizeFeature(FeatureHolder fh,
Feature.Template templ)
Realize a feature template. |
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 |
setSourceTerm(Term t)
Set the source ontology-term for this feature. |
void |
setType(java.lang.String type)
Change the type of this feature. |
void |
setTypeTerm(Term t)
Set the type ontology-term for this feature. |
java.lang.String |
toString()
|
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
SimpleFeature
on the given sequence.
The feature is created underneath the parent FeatureHolder
and populated directly from the template fields. However,
if the template annotation is the Annotation.EMPTY_ANNOTATION
,
an empty SimpleAnnotation
is attached to the feature instead.
sourceSeq
- the source sequenceparent
- the parent sequence or featuretemplate
- the template for the featureMethod Detail |
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protected SimpleFeatureHolder getFeatureHolder()
protected boolean featureHolderAllocated()
protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to
be transient and lazily instantiated. Be sure to register & unregister the
forwarder in the code that does the ChangeEvent handling in setter methods.
ChangeSupport cs = super.getChangeSupport(ct);
if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
someForwarder = new ChangeForwarder(...
this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
}
return cs;
getChangeSupport
in class AbstractChangeable
public Location getLocation()
Feature
The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.
getLocation
in interface Feature
public void setLocation(Location loc) throws ChangeVetoException
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.
setLocation
in interface Feature
loc
- the new Location for this feature
ChangeVetoException
- if the location can't be alteredpublic Term getTypeTerm()
Feature
OntoTools.ANY
in implementations which aren't ontology aware.
getTypeTerm
in interface Feature
public java.lang.String getType()
Feature
getType
in interface Feature
public void setType(java.lang.String type) throws ChangeVetoException
Feature
setType
in interface Feature
type
- new type String
ChangeVetoException
- if the type can't be alteredpublic void setTypeTerm(Term t) throws ChangeVetoException
Feature
setTypeTerm
in interface Feature
ChangeVetoException
- if changes are not allowedpublic java.lang.String getSource()
Feature
getSource
in interface Feature
public Term getSourceTerm()
Feature
OntoTools.ANY
in implementations which aren't ontology aware.
getSourceTerm
in interface Feature
public FeatureHolder getParent()
Feature
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.
getParent
in interface Feature
public void setSource(java.lang.String source) throws ChangeVetoException
Feature
setSource
in interface Feature
source
- the new source String
ChangeVetoException
- if the source can't be alteredpublic void setSourceTerm(Term t) throws ChangeVetoException
Feature
setSourceTerm
in interface Feature
ChangeVetoException
- if changes are not allowedpublic Sequence getSequence()
Feature
Sequence
object to which this feature
is (ultimately) attached. For top level features, this will be
equal to the FeatureHolder
returned by
getParent
.
getSequence
in interface Feature
public Annotation getAnnotation()
Annotatable
getAnnotation
in interface Annotatable
public SymbolList getSymbols()
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.
getSymbols
in interface Feature
public int countFeatures()
FeatureHolder
countFeatures
in interface FeatureHolder
public java.util.Iterator features()
Feature
features
in interface Feature
features
in interface FeatureHolder
public void removeFeature(Feature f) throws ChangeVetoException
FeatureHolder
removeFeature
in interface FeatureHolder
ChangeVetoException
- if this FeatureHolder does not support
feature removal or if the change was vetoedpublic boolean containsFeature(Feature f)
FeatureHolder
containsFeature
in interface FeatureHolder
f
- the Feature to check
public FeatureHolder filter(FeatureFilter ff)
FeatureHolder
FeatureFilter
.
filter
in interface FeatureHolder
ff
- the FeatureFilter
to apply.
filter
.public FeatureHolder filter(FeatureFilter ff, boolean recurse)
FeatureHolder
filter
in interface FeatureHolder
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.public Feature.Template makeTemplate()
Feature
makeTemplate
in interface Feature
protected void fillTemplate(Feature.Template ft)
public java.lang.String toString()
toString
in class java.lang.Object
public Feature realizeFeature(FeatureHolder fh, Feature.Template templ) throws BioException
RealizingFeatureHolder
createFeature
method of either
this FeatureHolder
or one of our child Features.
realizeFeature
in interface RealizingFeatureHolder
BioException
public Feature createFeature(Feature.Template temp) throws BioException, ChangeVetoException
FeatureHolder
createFeature
in interface FeatureHolder
BioException
- if something went wrong during creating the feature
ChangeVetoException
- if this FeatureHolder does not support
creation of new features, or if the change was vetoedpublic int hashCode()
hashCode
in class java.lang.Object
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public FeatureFilter getSchema()
FeatureHolder
FeatureHolder
. This is a filter
which all Feature
s 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))
.
getSchema
in interface FeatureHolder
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