Package org.biojava.bio.seq.impl

Class LazyFilterFeatureHolder

java.lang.Object
org.biojava.bio.seq.impl.LazyFilterFeatureHolder
All Implemented Interfaces:
FeatureHolder, Changeable
public class LazyFilterFeatureHolder extends Object implements FeatureHolder
FeatureHolder which lazily applies a specified filter to another FeatureHolder. This means that when you use a second filter to query the LazyFilterFeatureHolder, the underlying holder receives a single filter request with the two queries ANDed together.
Since:
1.3
Author:
Thomas Down

  • Constructor Details

  • Method Details

    • features

      public Iterator features()
      Description copied from interface: FeatureHolder
      Iterate over the features in no well defined order.
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • 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

    • 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

    • hasListeners

      protected boolean hasListeners()

    • getChangeSupport

      protected ChangeSupport getChangeSupport()

    • addChangeListener

      public final 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

    • addChangeListener

      public final 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 final 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

    • removeChangeListener

      public final 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

    • getSchema

      public FeatureFilter getSchema()
      Description copied from interface: FeatureHolder
      Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

      For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

      Specified by:
      getSchema in interface FeatureHolder
      Returns:
      the schema filter