Package org.biojava.bio.seq.impl

Class SimpleFramedFeature

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.impl.SimpleFeature

org.biojava.bio.seq.impl.SimpleStrandedFeature

org.biojava.bio.seq.impl.SimpleFramedFeature

All Implemented Interfaces:

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

public class SimpleFramedFeature
extends SimpleStrandedFeature
implements FramedFeature, Frame

Title: SimpleFramedFeature.

Description: A no frills implementation of FramedFeature.

Copyright: Copyright (c) 2001.

Version:

1.0

Author:

Mark Schreiber

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.FramedFeature

FramedFeature.ReadingFrame, FramedFeature.Template

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.Frame

FRAME_0, FRAME_1, FRAME_2

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

FRAME_0, FRAME_1, FRAME_2

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

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Constructor Summary

Constructors

Constructor	Description
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)

Method Summary

Modifier and Type	Method	Description
protected void	fillTemplate(FramedFeature.Template ft)
int	getFrame()	A method to get the frame information of the implementing object
FramedFeature.ReadingFrame	getReadingFrame()	return the reading frame of the feature.
Feature.Template	makeTemplate()	Create a new Template that could be used to generate a feature identical to this one.
String	toString()

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

fillTemplate, getStrand, getSymbols, setStrand

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

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

getStrand

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

getSymbols, setStrand

Constructor Detail

SimpleFramedFeature

public SimpleFramedFeature(Sequence sourceSeq,
                           FeatureHolder parent,
                           FramedFeature.Template template)
                    throws IllegalAlphabetException

Throws:

IllegalAlphabetException

Method Detail

getReadingFrame

public FramedFeature.ReadingFrame getReadingFrame()

Description copied from interface: FramedFeature

return the reading frame of the feature.

Specified by:

getReadingFrame in interface FramedFeature

getFrame

public int getFrame()

Description copied from interface: Frame

A method to get the frame information of the implementing object

Specified by:

getFrame in interface Frame

Returns:

an integer from 0 to 2 representing the frame.

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 SimpleStrandedFeature

Returns:

a new Template that would make a feature like this one

fillTemplate

protected void fillTemplate(FramedFeature.Template ft)

toString

public String toString()

Overrides:

toString in class SimpleStrandedFeature