Interface FeatureHolder

    • Field Detail

      • FEATURES

        static final ChangeType FEATURES
        Signals that features have been added or removed directly within this FeatureHolder.
      • SCHEMA

        static final ChangeType SCHEMA
        Signals that the schema of this FeatureHolder has changed.
        Since:
        1.3
      • EMPTY_FEATURE_HOLDER

        static final FeatureHolder EMPTY_FEATURE_HOLDER
    • Method Detail

      • countFeatures

        int countFeatures()
        Count how many features are contained.
        Returns:
        a positive integer or zero, equal to the number of features contained
      • features

        java.util.Iterator<Feature> features()
        Iterate over the features in no well defined order.
        Returns:
        an Iterator
      • filter

        FeatureHolder filter​(FeatureFilter fc,
                             boolean recurse)
        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.
        Parameters:
        fc - 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.
      • filter

        FeatureHolder filter​(FeatureFilter filter)
        Query this set of features using a supplied FeatureFilter.
        Parameters:
        filter - the FeatureFilter to apply.
        Returns:
        all features in this container which match filter.
      • createFeature

        Feature createFeature​(Feature.Template ft)
                       throws BioException,
                              ChangeVetoException
        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.
        Throws:
        BioException - if something went wrong during creating the feature
        ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed
      • containsFeature

        boolean containsFeature​(Feature f)
        Check if the feature is present in this holder.
        Parameters:
        f - the Feature to check
        Returns:
        true if f is in this set
        Since:
        1.2
      • getSchema

        FeatureFilter getSchema()
        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)).

        Returns:
        the schema filter
        Since:
        1.3