Class ProjectedFeatureHolder

  • All Implemented Interfaces:
    java.io.Serializable, FeatureHolder, Changeable

    public final class ProjectedFeatureHolder
    extends AbstractFeatureHolder
    implements FeatureHolder, java.io.Serializable
    Helper class for projecting Feature objects into an alternative coordinate system. This class offers a view onto a set of features, projecting them into a different coordinate system, and also changing their parent property. The destination coordinate system can run in the opposite direction from the source, in which case the strand property of StrandedFeatures is flipped.

    The projected features returned by this class are small proxy objects. Proxy classes are autogenerated on demand for any sub-interface of Feature by the ProjectionEngine class.

    Since:
    1.1
    Author:
    Thomas Down, Matthew Pocock
    See Also:
    Serialized Form
    • Constructor Detail

      • ProjectedFeatureHolder

        public ProjectedFeatureHolder​(ProjectionContext context)
    • Method Detail

      • features

        public java.util.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,
                                    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
        Overrides:
        filter in class AbstractFeatureHolder
        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.
      • 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
      • makeProjectionSet

        protected FeatureHolder makeProjectionSet​(FeatureHolder fh)
        Called internally to construct a lightweight projected view of a set of features
      • forwardChangeEvent

        protected ChangeEvent forwardChangeEvent​(ChangeEvent cev)
        Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder