Package org.biojava.bio.seq.projection

Class ProjectedFeature

java.lang.Object
org.biojava.bio.seq.projection.ProjectedFeature
All Implemented Interfaces:
Annotatable, Feature, FeatureHolder, Projection, Changeable
public abstract class ProjectedFeature extends Object implements Feature, Projection
Internal class used by ProjectionEngine to wrap Feature objects. This is not for you. This is the base class that the projection engine extends. If you modify this you will modify every projected feature. That is probably a bad thing.
Since:
1.1
Author:
Thomas Down, Matthew Pocock

  • Constructor Details

  • Method Details

    • getViewedFeature

      public Feature getViewedFeature()
      Specified by:
      getViewedFeature in interface Projection

    • getProjectionContext

      public ProjectionContext getProjectionContext()
      Specified by:
      getProjectionContext in interface Projection

    • getSequence

      public Sequence getSequence()
      Description copied from interface: Feature
      Return the Sequence object to which this feature is (ultimately) attached. For top level features, this will be equal to the FeatureHolder returned by getParent.
      Specified by:
      getSequence in interface Feature
      Returns:
      the ultimate parent Sequence

    • getParent

      public FeatureHolder getParent()
      Description copied from interface: Feature
      Return the FeatureHolder to which this feature has been attached. This will be a Sequence object for top level features, and a Feature object for features further down the tree.
      Specified by:
      getParent in interface Feature

    • getSymbols

      public SymbolList getSymbols()
      Description copied from interface: Feature
      Return a list of symbols that are contained in this feature.

      The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

      The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

      If the feature location is modified then this does not modify any SymbolList produced by earlier invocations of this method.

      Specified by:
      getSymbols in interface Feature
      Returns:
      a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

    • countFeatures

      public int countFeatures()
      Description copied from interface: FeatureHolder
      Count how many features are contained.
      Specified by:
      countFeatures in interface FeatureHolder
      Returns:
      a positive integer or zero, equal to the number of features contained

    • containsFeature

      public boolean containsFeature(Feature f)
      Description copied from interface: FeatureHolder
      Check if the feature is present in this holder.
      Specified by:
      containsFeature in interface FeatureHolder
      Parameters:
      f - the Feature to check
      Returns:
      true if f is in this set

    • getProjectedFeatures

      protected FeatureHolder getProjectedFeatures()

    • features

      public Iterator features()
      Description copied from interface: Feature
      Iterate over any child features which are held by this feature. The order of iteration MAY be significant for some types of Feature.
      Specified by:
      features in interface Feature
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • filter

      public FeatureHolder filter(FeatureFilter ff)
      Description copied from interface: FeatureHolder
      Query this set of features using a supplied FeatureFilter.
      Specified by:
      filter in interface FeatureHolder
      Parameters:
      ff - the FeatureFilter to apply.
      Returns:
      all features in this container which match filter.

    • filter

      public FeatureHolder filter(FeatureFilter ff, boolean recurse)
      Description copied from interface: FeatureHolder
      Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.
      Specified by:
      filter in interface FeatureHolder
      Parameters:
      ff - the FeatureFilter to apply
      recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

    • createFeature

      public Feature createFeature(Feature.Template temp) throws ChangeVetoException, BioException
      Description copied from interface: FeatureHolder
      Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.
      Specified by:
      createFeature in interface FeatureHolder
      Throws:
      ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed
      BioException - if something went wrong during creating the feature

    • removeFeature

      public void removeFeature(Feature f) throws ChangeVetoException, BioException
      Description copied from interface: FeatureHolder
      Remove a feature from this FeatureHolder.
      Specified by:
      removeFeature in interface FeatureHolder
      Throws:
      ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed
      BioException - if there was an error removing the feature

    • 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
      Returns:
      a new Template that would make a feature like this one

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • addChangeListener

      public void addChangeListener(ChangeListener cl)
      Description copied from interface: Changeable
      Add a listener that will be informed of all changes.
      Specified by:
      addChangeListener in interface Changeable
      Parameters:
      cl - the ChangeListener to add

    • removeChangeListener

      public void removeChangeListener(ChangeListener cl)
      Description copied from interface: Changeable
      Remove a listener that was interested in all types of changes.
      Specified by:
      removeChangeListener in interface Changeable
      Parameters:
      cl - a ChangeListener to remove

    • addChangeListener

      public void addChangeListener(ChangeListener cl, ChangeType ct)
      Description copied from interface: Changeable
      Add a listener that will be informed of changes of a given type.
      Specified by:
      addChangeListener in interface Changeable
      Parameters:
      cl - the ChangeListener
      ct - the ChangeType it is to be informed of

    • removeChangeListener

      public void removeChangeListener(ChangeListener cl, ChangeType ct)
      Description copied from interface: Changeable
      Remove a listener that was interested in a specific types of changes.
      Specified by:
      removeChangeListener in interface Changeable
      Parameters:
      cl - a ChangeListener to remove
      ct - the ChangeType that it was interested in

    • isUnchanging

      public boolean isUnchanging(ChangeType ct)
      Description copied from interface: Changeable

      A particular ChangeType can never be raised by this Changeable.

      If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

      Specified by:
      isUnchanging in interface Changeable
      Parameters:
      ct - the ChangeType to check
      Returns:
      true if ChangeEvents of this type are guaranteed to never be fired