Package org.biojava.bio.seq.impl

Class SimpleStrandedFeature

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.impl.SimpleFeature

org.biojava.bio.seq.impl.SimpleStrandedFeature

All Implemented Interfaces:

Serializable, Annotatable, Feature, FeatureHolder, RealizingFeatureHolder, StrandedFeature, Changeable

Direct Known Subclasses:

SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleSimilarityPairFeature

public class SimpleStrandedFeature
extends SimpleFeature
implements StrandedFeature

A no-frills implementation of StrandedFeature.

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

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

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand, StrandedFeature.Template

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

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Constructor Summary

Constructors

Constructor	Description
SimpleStrandedFeature(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template)

Method Summary

Modifier and Type	Method	Description
protected void	fillTemplate(StrandedFeature.Template ft)
StrandedFeature.Strand	getStrand()	Retrieve the strand that this feature lies upon.
SymbolList	getSymbols()	Return a list of symbols that are contained in this feature.
Feature.Template	makeTemplate()	Create a new Template that could be used to generate a feature identical to this one.
void	setStrand(StrandedFeature.Strand strand)	Set the strand that this feature lies upon.
String	toString()

Methods inherited from class org.biojava.bio.seq.impl.SimpleFeature

containsFeature, countFeatures, createFeature, equals, featureHolderAllocated, features, fillTemplate, filter, filter, getAnnotation, getChangeSupport, getFeatureHolder, getLocation, getParent, getSchema, getSequence, getSource, getSourceTerm, getType, getTypeTerm, hashCode, realizeFeature, removeFeature, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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 org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Constructor Detail

SimpleStrandedFeature

public SimpleStrandedFeature(Sequence sourceSeq,
                             FeatureHolder parent,
                             StrandedFeature.Template template)
                      throws IllegalArgumentException

Throws:

IllegalArgumentException

Method Detail

getStrand

public StrandedFeature.Strand getStrand()

Description copied from interface: StrandedFeature

Retrieve the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Specified by:

getStrand in interface StrandedFeature

Returns:

one of the Strand constants

getSymbols

public SymbolList 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 interface Feature

Specified by:

getSymbols in interface StrandedFeature

Overrides:

getSymbols in class SimpleFeature

Returns:

a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

setStrand

public void setStrand(StrandedFeature.Strand strand)
               throws ChangeVetoException

Description copied from interface: StrandedFeature

Set the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Specified by:

setStrand in interface StrandedFeature

Parameters:

strand - a Strand.

Throws:

ChangeVetoException - if the strand may not be changed.

makeTemplate

public Feature.Template 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 interface Feature

Overrides:

makeTemplate in class SimpleFeature

Returns:

a new Template that would make a feature like this one

fillTemplate

protected void fillTemplate(StrandedFeature.Template ft)

toString

public String toString()

Overrides:

toString in class SimpleFeature