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
static class FramedFeature.ReadingFrame
          A singleton to hold the frame information
static class FramedFeature.Template
           
 
Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand
 
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.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
static FramedFeature.ReadingFrame FRAME_0
           
static FramedFeature.ReadingFrame FRAME_1
           
static FramedFeature.ReadingFrame FRAME_2
           
 
Fields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
 
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.Annotatable
ANNOTATION
 
Method Summary
 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.seq.StrandedFeature
getSymbols, setStrand
 
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.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

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