Package org.biojava.bio.seq.impl

Class SimpleFeature

    • Constructor Detail

      • SimpleFeature

        public SimpleFeature​(Sequence sourceSeq,
                     FeatureHolder parent,
                     Feature.Template template)
        Create a SimpleFeature on the given sequence. The feature is created underneath the parent FeatureHolder and populated directly from the template fields. However, if the template annotation is the Annotation.EMPTY_ANNOTATION, an empty SimpleAnnotation is attached to the feature instead.
        Parameters:
        sourceSeq - the source sequence
        parent - the parent sequence or feature
        template - the template for the feature

    • Method Detail

      • getFeatureHolder

        protected SimpleFeatureHolder getFeatureHolder()
        A utility function to retrieve the feature holder delegate, creating it if necessary.
        Returns:
        the FeatureHolder delegate

      • featureHolderAllocated

        protected boolean featureHolderAllocated()
        A utility function to find out if the feature holder delegate has been instantiated yet. If it has not, we may avoid instantiating it by returning some pre-canned result.
        Returns:
        true if the feature holder delegate has been created and false otherwise

      • 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

      • getLocation

        public Location getLocation()
        Description copied from interface: Feature
        The location of this feature.

        The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.

        Specified by:
        getLocation in interface Feature
        Returns:
        a Location anchoring this feature

      • setLocation

        public void setLocation​(Location loc)
                 throws ChangeVetoException
        Description copied from interface: Feature
        The new location for this feature.

        The location may be complicated or simply a range. The annotation is assumed to apply to the entire region contained within the location. Any values returned from methods that rely on the old location must not be affected.

        Specified by:
        setLocation in interface Feature
        Parameters:
        loc - the new Location for this feature
        Throws:
        ChangeVetoException - if the location can't be altered

      • getTypeTerm

        public Term getTypeTerm()
        Description copied from interface: Feature
        An ontology term defining the type of feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.
        Specified by:
        getTypeTerm in interface Feature

      • getType

        public String getType()
        Description copied from interface: Feature
        The type of the feature.
        Specified by:
        getType in interface Feature
        Returns:
        the type of this sequence

      • getSource

        public String getSource()
        Description copied from interface: Feature
        The source of the feature. This may be a program or process.
        Specified by:
        getSource in interface Feature
        Returns:
        the source, or generator

      • getSourceTerm

        public Term getSourceTerm()
        Description copied from interface: Feature
        An ontology term defining the source of this feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.
        Specified by:
        getSourceTerm in interface Feature

      • 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

      • 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

      • 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

      • 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