org.biojava.bio.seq.impl
Class SimpleFramedFeature

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.seq.impl.SimpleFeature
          extended by org.biojava.bio.seq.impl.SimpleStrandedFeature
              extended by 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.seq.FramedFeature
FramedFeature.ReadingFrame, 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
 
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
 
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
 
Fields inherited from interface org.biojava.bio.seq.Frame
FRAME_0, FRAME_1, FRAME_2
 
Constructor Summary
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)
           
 
Method Summary
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.seq.FramedFeature
getStrand
 
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, 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.Annotatable
getAnnotation
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

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