Class RestrictionMapper
- All Implemented Interfaces:
SequenceAnnotator
RestrictionMapper
is a class for annotating
Sequence
s with Feature
s which represent
restriction sites. Calling annotate(Sequence sequence)
will annotate the Sequence
with the sites of any
RestrictionEnzyme
s which have been added to the
RestrictionMapper
. The returned Sequence
is a ViewSequence
wrapping the original.
The Feature
s created are
RestrictionSite
s 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
RestrictionEnzyme
s to be searched must first be
registered with the RestrictionEnzymeManager
.
- Since:
- 1.3
- Author:
- Keith James
-
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionCreates a newRestrictionMapper
which will use the specifiedExecutorService
.RestrictionMapper
(ThreadPool threadPool) Creates a newRestrictionMapper
which will use the specifiedThreadPool
. -
Method Summary
Modifier and TypeMethodDescriptionvoid
addEnzyme
(RestrictionEnzyme enzyme) addEnzyme
adds an enzyme to be searched for in theSequence
.annotate
addsFeature
s which represent restriction sites.void
clearEnzymes
removes all enzymes from those to be searched for in theSequence
.boolean
getMapAll
returns whether all sites should be marked, including those which have recognition sites within the sequence, but cut outside it.void
removeEnzyme
(RestrictionEnzyme enzyme) removeEnzyme
removes an enzyme from those to be searched for in theSequence
.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.
-
Field Details
-
SITE_FEATURE_SOURCE
SITE_FEATURE_SOURCE
the sourceString
used byRestrictionMapper
when creating restriction siteFeature
s. This is theString
which is returned when aFeature
'sgetSource()
method is called.- See Also:
-
SITE_FEATURE_TYPE
SITE_FEATURE_TYPE
the typeString
used byRestrictionMapper
when creating restriction siteFeature
s. This is theString
which is returned when aFeature
'sgetType()
method is called.- See Also:
-
-
Constructor Details
-
RestrictionMapper
Creates a new
RestrictionMapper
which will use the specifiedThreadPool
. Do not share one pool between a number ofRestrictionMapper
s becauseannotate(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
- aThreadPool
.
-
RestrictionMapper
Creates a new
RestrictionMapper
which will use the specifiedExecutorService
.- Parameters:
xser
- aExecutorService
, e.g. ExecutorService.newCachedThreadPool()- Since:
- 1.8.1
-
-
Method Details
-
annotate
annotate
addsFeature
s which represent restriction sites.- Specified by:
annotate
in interfaceSequenceAnnotator
- Parameters:
sequence
- aSequence
.- Returns:
- a
Sequence
view with restriction sites marked.
-
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
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
- aboolean
.
-
addEnzyme
addEnzyme
adds an enzyme to be searched for in theSequence
.- Parameters:
enzyme
- aRestrictionEnzyme
.
-
removeEnzyme
removeEnzyme
removes an enzyme from those to be searched for in theSequence
.- Parameters:
enzyme
- aRestrictionEnzyme
.
-
clearEnzymes
clearEnzymes
removes all enzymes from those to be searched for in theSequence
.
-