Package org.biojava.bio.seq

Interface FramedFeature

All Superinterfaces:

Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature

All Known Implementing Classes:

SimpleFramedFeature

public interface FramedFeature
extends StrandedFeature

Title: FramedFeature.

Description: An feature that includes the concept of frame by extending stranded.

Copyright: Copyright (c) 2001

Version:

1.0

Author:

Mark Schreiber

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	FramedFeature.ReadingFrame	A singleton to hold the frame information
static class	FramedFeature.Template

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

Fields

Modifier and Type	Field	Description
static FramedFeature.ReadingFrame	FRAME_0
static FramedFeature.ReadingFrame	FRAME_1
static FramedFeature.ReadingFrame	FRAME_2

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

Method Summary

Modifier and Type	Method	Description
FramedFeature.ReadingFrame	getReadingFrame()	return the reading frame of the feature.
StrandedFeature.Strand	getStrand()	Retrieve the strand that this feature lies upon.

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, 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.biojava.bio.seq.StrandedFeature

getSymbols, setStrand

Field Detail

FRAME_0

static final FramedFeature.ReadingFrame FRAME_0

FRAME_1

static final FramedFeature.ReadingFrame FRAME_1

FRAME_2

static final FramedFeature.ReadingFrame FRAME_2

Method Detail

getReadingFrame

FramedFeature.ReadingFrame getReadingFrame()

return the reading frame of the feature.

getStrand

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:

the Strand that the feature is found on