Package org.biojava.bio.molbio

Class RestrictionMapper

  • All Implemented Interfaces:
    SequenceAnnotator
    public class RestrictionMapper
extends Object
implements SequenceAnnotator

    RestrictionMapper is a class for annotating Sequences with Features which represent restriction sites. Calling annotate(Sequence sequence) will annotate the Sequence with the sites of any RestrictionEnzymes which have been added to the RestrictionMapper. The returned Sequence is a ViewSequence wrapping the original.

    The Features created are RestrictionSites which have a flyweight Annotation containing a single String property "dbxref" whose value is "REBASE:" plus name of the enzyme (e.g. EcoRI).

    The mapper will by default map only those sites which have both their recognition sites and their cut sites within the Sequence. This behaviour may be changed to map all sites which have their recognition sites within the Sequence using the setMapAll(boolean on) method.

    The current implementation requires that RestrictionEnzymes to be searched must first be registered with the RestrictionEnzymeManager.

    Since:
    1.3
    Author:
    Keith James

    • Field Detail

      • SITE_FEATURE_SOURCE

        public static final String SITE_FEATURE_SOURCE
        SITE_FEATURE_SOURCE the source String used by RestrictionMapper when creating restriction site Features. This is the String which is returned when a Feature's getSource() method is called.
        See Also:
        Constant Field Values

      • SITE_FEATURE_TYPE

        public static final String SITE_FEATURE_TYPE
        SITE_FEATURE_TYPE the type String used by RestrictionMapper when creating restriction site Features. This is the String which is returned when a Feature's getType() method is called.
        See Also:
        Constant Field Values

    • Constructor Detail

      • RestrictionMapper

        public RestrictionMapper​(ThreadPool threadPool)

        Creates a new RestrictionMapper which will use the specified ThreadPool. Do not share one pool between a number of RestrictionMappers because annotate(Sequence sequence) waits for all threads in the pool to finish work before returning and this will lead to a race condition between mappers. One mapper could end up waiting for another mapper's threads before returning.

        Parameters:
        threadPool - a ThreadPool.

      • RestrictionMapper

        public RestrictionMapper​(ExecutorService xser)

        Creates a new RestrictionMapper which will use the specified ExecutorService.

        Parameters:
        xser - a ExecutorService, e.g. ExecutorService.newCachedThreadPool()
        Since:
        1.8.1

    • Method Detail

      • annotate

        public Sequence annotate​(Sequence sequence)
        annotate adds Features which represent restriction sites.
        Specified by:
        annotate in interface SequenceAnnotator
        Parameters:
        sequence - a Sequence.
        Returns:
        a Sequence view with restriction sites marked.

      • getMapAll

        public boolean getMapAll()
        getMapAll returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it. The default is false, indicating only sites which can actually be cut are mapped.
        Returns:
        a boolean.

      • setMapAll

        public void setMapAll​(boolean on)
        setMapAll sets whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it. The default is false, indicating only sites which can actually be cut are mapped.
        Parameters:
        on - a boolean.

      • addEnzyme

        public void addEnzyme​(RestrictionEnzyme enzyme)
        addEnzyme adds an enzyme to be searched for in the Sequence.
        Parameters:
        enzyme - a RestrictionEnzyme.

      • removeEnzyme

        public void removeEnzyme​(RestrictionEnzyme enzyme)
        removeEnzyme removes an enzyme from those to be searched for in the Sequence.
        Parameters:
        enzyme - a RestrictionEnzyme.

      • clearEnzymes

        public void clearEnzymes()
        clearEnzymes removes all enzymes from those to be searched for in the Sequence.