Class SimpleGappedSequence

    • Constructor Detail

      • SimpleGappedSequence

        public SimpleGappedSequence​(Sequence seq)
      • SimpleGappedSequence

        public SimpleGappedSequence​(GappedSequence seq)
    • Method Detail

      • getCreateOnUnderlyingSequence

        public boolean getCreateOnUnderlyingSequence()
      • setCreateOnUnderlyingSequence

        public void setCreateOnUnderlyingSequence​(boolean underlying)
      • getAnnotation

        public Annotation getAnnotation()
        Description copied from interface: Annotatable
        Should return the associated annotation object.
        Specified by:
        getAnnotation in interface Annotatable
        Returns:
        an Annotation object, never null
      • getName

        public java.lang.String getName()
        Description copied from interface: Sequence
        The name of this sequence.

        The name may contain spaces or odd characters.

        Specified by:
        getName in interface Sequence
        Returns:
        the name as a String
      • getURN

        public java.lang.String getURN()
        Description copied from interface: Sequence
        A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g.
         urn:sequence/embl:AL121903
         
        It may also be a URL identifying a specific resource, either locally or over the network
         file:///home/thomas/myseq.fa|seq22
         http://www.mysequences.net/chr22.seq
         
        Specified by:
        getURN in interface Sequence
        Returns:
        the URI as a String
      • 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
      • 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.
      • 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
      • 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