Package org.biojavax.bio.seq
Interface RichFeature
- All Superinterfaces:
Annotatable,Changeable,Comparable,Feature,FeatureHolder,RankedCrossRefable,RichAnnotatable,RichFeatureRelationshipHolder,StrandedFeature
- All Known Implementing Classes:
SimpleRichFeature
public interface RichFeature
extends StrandedFeature, RankedCrossRefable, RichAnnotatable, RichFeatureRelationshipHolder, Comparable
Represents a feature that can be given name and rank and be
moved from one sequence to another.
- Since:
- 1.5
- Author:
- Richard Holland
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic classAdded-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases.static classSome useful tools for working with features.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarderNested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparatorNested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolderNested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final ChangeTypestatic final ChangeTypestatic final ChangeTypestatic final ChangeTypestatic final ChangeTypestatic final ChangeTypestatic final ChangeTypestatic final ChangeTypeFields inherited from interface org.biojava.bio.Annotatable
ANNOTATIONFields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, PROPERTY_DATA_KEY, SOURCE, TYPEFields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMAFields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN -
Method Summary
Modifier and TypeMethodDescriptiongetName()Returns the name of this feature.intgetRank()Returns the rank of this feature.voidSets the name of this feature.voidsetParent(FeatureHolder parent) Sets the parent of this feature.voidsetRank(int rank) Sets the rank of this feature.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotationMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from interface java.lang.Comparable
compareToMethods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTermMethods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeatureMethods inherited from interface org.biojavax.RankedCrossRefable
addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefsMethods inherited from interface org.biojavax.RichAnnotatable
getNoteSet, getRichAnnotation, setNoteSetMethods inherited from interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
addFeatureRelationship, getFeatureRelationshipSet, removeFeatureRelationship, setFeatureRelationshipSetMethods inherited from interface org.biojava.bio.seq.StrandedFeature
getStrand, getSymbols, setStrand
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Field Details
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NAME
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RANK
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SOURCETERM
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TYPETERM
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LOCATION
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PARENT
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CROSSREF
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RELATION
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Method Details
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setParent
Sets the parent of this feature.- Parameters:
parent- the parent the feature should identify itself with.- Throws:
ChangeVetoException- if the new value is unacceptable.
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getName
Returns the name of this feature.- Returns:
- the name.
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setName
Sets the name of this feature.- Parameters:
name- the name the feature should identify itself with.- Throws:
ChangeVetoException- if the new value is unacceptable.
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getRank
int getRank()Returns the rank of this feature.- Returns:
- the rank.
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setRank
Sets the rank of this feature.- Parameters:
rank- the rank the feature should identify itself with.- Throws:
ChangeVetoException- if the new value is unacceptable.
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