Package org.biojava.bio.seq.projection

Class 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

    • Method Detail

      • 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

      • 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.

      • 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

      • 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