org.biojava.bio.seq.projection.ReparentContext

All Implemented Interfaces:: Serializable, ProjectionContext

Direct Known Subclasses:: SimpleGappedSequence.GappedContext, SubSequence.SubProjectedFeatureContext, TranslateFlipContext

public class ReparentContext extends Object implements ProjectionContext, Serializable

A good base class to implement ProjectionContext from.

ReparentContext takes care of much of the ugliness of implementing ProjectionContext, such as handling listeners and grafting features onto a new parent. It also sets up a framework for mutating feature filters. Think carefully before overriding methods in this class.

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor

Description

ReparentContext(FeatureHolder parent, FeatureHolder wrapped)
Method Summary

Modifier and Type

Method

Description

final void

addChangeListener(Feature f, ChangeListener cl, ChangeType ct)

Add a ChangeListener to a projected feature.

final Feature

createFeature(Feature.Template projTempl)

Create a projected feature with properties matching the template.

final Feature

createFeature(Feature f, Feature.Template projTempl)

Create a new projected feature.

final FeatureHolder

getParent()

final FeatureHolder

getParent(Feature f)

protected FilterUtils.FilterTransformer

getReverter()

final FeatureFilter

getSchema(Feature f)

final Sequence

getSequence(Feature f)

Get the sequence for a feature.

protected FilterUtils.FilterTransformer

getTransformer()

final FeatureHolder

getUnprojectedFeatures()

Get the features before projection.

FeatureHolder

projectChildFeatures(Feature f, FeatureHolder parent)

Project all features that are children of feature so that they become children of parent.

Feature

projectFeature(Feature feat)

Create a single projected feature using the rules of this ProjectedFeatureHolder.

final FeatureHolder

projectFeatures(FeatureHolder fh)

Project all of the features in a FeatureHolder.

final FeatureFilter

projectFilter(FeatureFilter ff)

Transform a filter on unprojected features so that it applies to projected features.

final void

removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)

Remove a ChangeListener from a projected feature.

final void

removeFeature(Feature dyingChild)

Remove the dying child.

final void

removeFeature(Feature f, Feature f2)

Remove the dying child.

Feature

revertFeature(Feature feat)

Unproject a feature.

final FeatureFilter

revertFilter(FeatureFilter ff)

Transform a filter on projected features so that it applies to unprojected features.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- ReparentContext
  
  public ReparentContext(FeatureHolder parent, FeatureHolder wrapped)
Method Details
- getParent
  
  public final FeatureHolder getParent()
- getUnprojectedFeatures
  
  public final FeatureHolder getUnprojectedFeatures()
  
  Description copied from interface: ProjectionContext
  
  Get the features before projection.
  If you are projecting all the features in some feature holder, that is what this method should return.
  
  Specified by:
  
  getUnprojectedFeatures in interface ProjectionContext
  
  Returns:
  
  the features before projection
- projectFeature
  
  public Feature projectFeature(Feature feat)
  
  Create a single projected feature using the rules of this ProjectedFeatureHolder.
  
  Specified by:
  
  projectFeature in interface ProjectionContext
  
  Parameters:
  
  feat - the Feature to project
  
  Returns:
  
  a Feature representing feat after being transformed by this context
- revertFeature
  
  public Feature revertFeature(Feature feat)
  
  Description copied from interface: ProjectionContext
  
  Unproject a feature.
  This is the inverse opperation to @link projectFeature().
  
  Note: The result of calling this method for a feature that is not projected through this context is not specified by this API, but it is reasonable to assume that bad things will happen.
  
  Specified by:
  
  revertFeature in interface ProjectionContext
  
  Parameters:
  
  feat - the Feature to un-project
  
  Returns:
  
  the unprojected feature
- projectFilter
  
  public final FeatureFilter projectFilter(FeatureFilter ff)
  
  Description copied from interface: ProjectionContext
  
  Transform a filter on unprojected features so that it applies to projected features.
  
  Specified by:
  
  projectFilter in interface ProjectionContext
  
  Parameters:
  
  ff - the FeatureFilter to transform
  
  Returns:
  
  the transformed FeatureFilter
- revertFilter
  
  public final FeatureFilter revertFilter(FeatureFilter ff)
  
  Description copied from interface: ProjectionContext
  
  Transform a filter on projected features so that it applies to unprojected features.
  
  Specified by:
  
  revertFilter in interface ProjectionContext
  
  Parameters:
  
  ff - the FeatureFilter to transform
  
  Returns:
  
  the transformed FeatureFilter
- getTransformer
  
  protected FilterUtils.FilterTransformer getTransformer()
- getReverter
  
  protected FilterUtils.FilterTransformer getReverter()
- getParent
  
  public final FeatureHolder getParent(Feature f)
  
  Specified by:
  
  getParent in interface ProjectionContext
- getSequence
  
  public final Sequence getSequence(Feature f)
  
  Description copied from interface: ProjectionContext
  
  Get the sequence for a feature.
  This will be the return value of projFeat.getParent().
  
  Specified by:
  
  getSequence in interface ProjectionContext
  
  Parameters:
  
  f - the projected Feature
  
  Returns:
  
  the Sequence of the Feature
- projectChildFeatures
  
  public FeatureHolder projectChildFeatures(Feature f, FeatureHolder parent)
  
  Description copied from interface: ProjectionContext
  
  Project all features that are children of feature so that they become children of parent.
  
  Specified by:
  
  projectChildFeatures in interface ProjectionContext
  
  Parameters:
  
  f - the Feature to project all children of
  
  parent - the new parent feature holder
  
  Returns:
  
  a FeatureHolder containing projections of all children of feature so that f.getParent() is equal to parent
- createFeature
  
  public final Feature createFeature(Feature.Template projTempl) throws BioException, ChangeVetoException
  
  Description copied from interface: ProjectionContext
  
  Create a projected feature with properties matching the template.
  You will probably implement this by delegating to the unprojected feature holder. It is imperative that the template properties are unprojected first so that when the newly created feature is projected, the properties match up.
  Not every projection context has fully reversible semantics. Use your discression and come up with a reasonable plan that causes least supprise to the user.
  
  Specified by:
  
  createFeature in interface ProjectionContext
  
  Parameters:
  
  projTempl - the Feature.Template to instantiate
  
  Returns:
  
  a new projected Feature matching the template as closely as possible
  
  Throws:
  
  BioException - if there was a problem instantiating the template
  
  ChangeVetoException - if the feature creation was vetoed
- removeFeature
  
  public final void removeFeature(Feature dyingChild) throws BioException, ChangeVetoException
  
  Description copied from interface: ProjectionContext
  
  Remove the dying child.
  
  Specified by:
  
  removeFeature in interface ProjectionContext
  
  Parameters:
  
  dyingChild - a projected feature to remove
  
  Throws:
  
  BioException - if there is an error removing the feature
  
  ChangeVetoException - if the removal of the feature was vetoed
- createFeature
  
  public final Feature createFeature(Feature f, Feature.Template projTempl) throws BioException, ChangeVetoException
  
  Description copied from interface: ProjectionContext
  
  Create a new projected feature.
  See the notes for @link createFeature(Feature.Template) for implementation advice.
  
  Specified by:
  
  createFeature in interface ProjectionContext
  
  Parameters:
  
  f - the parent for the newly created feature
  
  projTempl - the Feature.Template specifying the new feature
  
  Returns:
  
  a new ProjectedFeature that is a child of projParent
  
  Throws:
  
  BioException - if there was a problem creating the feature
  
  ChangeVetoException - if the creation of the feature was vetoed
- removeFeature
  
  public final void removeFeature(Feature f, Feature f2) throws ChangeVetoException, BioException
  
  Description copied from interface: ProjectionContext
  
  Remove the dying child.
  
  Specified by:
  
  removeFeature in interface ProjectionContext
  
  Parameters:
  
  f - the projected parent Feature
  
  f2 - the child Feature to remove
  
  Throws:
  
  ChangeVetoException - if the removal of the feature was vetoed
  
  BioException
- getSchema
  
  public final FeatureFilter getSchema(Feature f)
- addChangeListener
  
  public final void addChangeListener(Feature f, ChangeListener cl, ChangeType ct)
  
  Description copied from interface: ProjectionContext
  
  Add a ChangeListener to a projected feature.
  
  Specified by:
  
  addChangeListener in interface ProjectionContext
  
  Parameters:
  
  f - the projected Feature to add the listener for
  
  cl - the ChangeListener to add
  
  ct - the ChangeType to register it for
- removeChangeListener
  
  public final void removeChangeListener(Feature f, ChangeListener cl, ChangeType ct)
  
  Description copied from interface: ProjectionContext
  
  Remove a ChangeListener from a projected feature.
  
  Specified by:
  
  removeChangeListener in interface ProjectionContext
  
  Parameters:
  
  f - the projected Feature to remove the listener for
  
  cl - the ChangeListener to remove
  
  ct - the ChangeType it is registered for
- projectFeatures
  
  public final FeatureHolder projectFeatures(FeatureHolder fh)
  
  Description copied from interface: ProjectionContext
  
  Project all of the features in a FeatureHolder.
  Warning: The results of calling this method for features that are not in getUnprojectedFeatures() is not specified by this API, but it is reasonable to assume that bad things will happen.
  
  Specified by:
  
  projectFeatures in interface ProjectionContext
  
  Parameters:
  
  fh - the FeatureHolder containing the features to project
  
  Returns:
  
  a FeatureHolder containing all the features projected

Class ReparentContext

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

ReparentContext

Method Details

getParent

getUnprojectedFeatures

projectFeature

revertFeature

projectFilter

revertFilter

getTransformer

getReverter

getParent

getSequence

projectChildFeatures

createFeature

removeFeature

createFeature

removeFeature

getSchema

addChangeListener

removeChangeListener

projectFeatures