Package org.biojava.bio.seq
Interface FeatureHolder
- All Superinterfaces:
Changeable
- All Known Subinterfaces:
ComponentFeature
,Feature
,FramedFeature
,GappedSequence
,HomologyFeature
,RealizingFeatureHolder
,RemoteFeature
,RestrictionSite
,RichFeature
,RichSequence
,Sequence
,SimilarityPairFeature
,StrandedFeature
- All Known Implementing Classes:
AbstractFeatureHolder
,CircularView
,DummySequence
,FeatureHolder.EmptyFeatureHolder
,LazyFeatureHolder
,LazyFilterFeatureHolder
,MergeFeatureHolder
,NewSimpleAssembly
,PhredSequence
,ProjectedFeature
,ProjectedFeatureHolder
,RevCompSequence
,SimpleAssembly
,SimpleFeature
,SimpleFeatureHolder
,SimpleFramedFeature
,SimpleGappedSequence
,SimpleHomologyFeature
,SimpleRemoteFeature
,SimpleRestrictionSite
,SimpleRichFeature
,SimpleRichSequence
,SimpleSequence
,SimpleSimilarityPairFeature
,SimpleStrandedFeature
,SubSequence
,ThinRichSequence
,ViewSequence
The interface for objects that contain features.
Feature holders abstract the containment of a feature from the objects that implements both the real container or the features. FeatureHolders are like sets of features.
- Author:
- Matthew Pocock, Thomas Down
- See Also:
-
Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final FeatureHolder
static final ChangeType
Signals that features have been added or removed directly within this FeatureHolder.static final ChangeType
Signals that the schema of this FeatureHolder has changed. -
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 filter) 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 interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
-
Field Details
-
FEATURES
Signals that features have been added or removed directly within this FeatureHolder. -
SCHEMA
Signals that the schema of this FeatureHolder has changed.- Since:
- 1.3
-
EMPTY_FEATURE_HOLDER
-
-
Method Details
-
countFeatures
int countFeatures()Count how many features are contained.- Returns:
- a positive integer or zero, equal to the number of features contained
-
features
Iterate over the features in no well defined order.- Returns:
- an Iterator
-
filter
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.- 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.
-
filter
Query this set of features using a suppliedFeatureFilter
.- Parameters:
filter
- theFeatureFilter
to apply.- Returns:
- all features in this container which match
filter
.
-
createFeature
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.- Throws:
BioException
- if something went wrong during creating the featureChangeVetoException
- if this FeatureHolder does not support creation of new features, or if the change was vetoed
-
removeFeature
Remove a feature from this FeatureHolder.- Throws:
ChangeVetoException
- if this FeatureHolder does not support feature removal or if the change was vetoedBioException
- if there was an error removing the feature
-
containsFeature
Check if the feature is present in this holder.- Parameters:
f
- the Feature to check- Returns:
- true if f is in this set
- Since:
- 1.2
-
getSchema
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))
.- Returns:
- the schema filter
- Since:
- 1.3
-