Package org.biojava.bio.seq

Class LazyFeatureHolder

  • All Implemented Interfaces:
    FeatureHolder, Changeable
    public abstract class LazyFeatureHolder
extends AbstractChangeable
implements FeatureHolder
    Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand. This is an abstract class and is normally used like: FeatureHolder fh = new LazyFeatureHolder() { protected FeatureHolder createFeatureHolder() { SimpleFeatureHolder features = new SimpleFeatureHolder(); // Create some features in here... return features; } } ;
    Since:
    1.2
    Author:
    Thomas Down, Matthew Pocock
    See Also:
    RichFeatureRelationshipHolder

    • Constructor Detail

      • LazyFeatureHolder

        protected LazyFeatureHolder()
        Construct a LazyFeatureHolder with the schema of its contained featureholder

    • Method Detail

      • 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

      • 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

      • 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.

      • getChangeSupport

        protected ChangeSupport getChangeSupport​(ChangeType ct)
        Description copied from class: AbstractChangeable
        Called to retrieve the ChangeSupport for this object.

        Your implementation of this method should have the following structure: 

         ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
        It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
        Overrides:
        getChangeSupport in class AbstractChangeable