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
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
Added-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 class
Some useful tools for working with features.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
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
static final ChangeType
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, PROPERTY_DATA_KEY, SOURCE, TYPE
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
-
Method Summary
Modifier and TypeMethodDescriptiongetName()
Returns the name of this feature.int
getRank()
Returns the rank of this feature.void
Sets the name of this feature.void
setParent
(FeatureHolder parent) Sets the parent of this feature.void
setRank
(int rank) Sets the rank of this feature.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface java.lang.Comparable
compareTo
Methods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature
Methods inherited from interface org.biojavax.RankedCrossRefable
addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefs
Methods inherited from interface org.biojavax.RichAnnotatable
getNoteSet, getRichAnnotation, setNoteSet
Methods inherited from interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
addFeatureRelationship, getFeatureRelationshipSet, removeFeatureRelationship, setFeatureRelationshipSet
Methods inherited from interface org.biojava.bio.seq.StrandedFeature
getStrand, getSymbols, setStrand
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Field Details
-
NAME
-
RANK
-
SOURCETERM
-
TYPETERM
-
LOCATION
-
PARENT
-
CROSSREF
-
RELATION
-
-
Method Details
-
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.
-
getName
Returns the name of this feature.- Returns:
- the name.
-
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.
-
getRank
int getRank()Returns the rank of this feature.- Returns:
- the rank.
-
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.
-