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.

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 Details
- SimpleFramedFeature
  
  public SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template) throws IllegalAlphabetException
  
  Throws:
  
  IllegalAlphabetException
Method Details
- 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

Class SimpleFramedFeature

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

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

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

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

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

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

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

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

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

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.bio.Annotatable

Methods inherited from interface org.biojava.utils.Changeable

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

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

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

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

Constructor Details

SimpleFramedFeature

Method Details

getReadingFrame

getFrame

makeTemplate

fillTemplate

toString