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java.lang.Objectorg.biojava.bio.molbio.RestrictionEnzymeManager
RestrictionEnzymeManager
manages collections of
static RestrictionEnzyme
instances. A properties file
should be placed in the CLASSPATH containing a key
"rebase.data.file" and a corresponding value of a REBASE file
(standard REBASE format #31 conventionally named withrefm.### where
### is the version number). This file will be loaded by the
RestrictionEnzymeManager
ClassLoader
. The
properties are loaded as a ResourceBundle
, so the file
should be named "RestrictionEnzymeManager.properties".
Field Summary | |
static java.lang.String |
REBASE_DATA_KEY
REBASE_DATA_KEY the ResourceBundle key which
specifies the location of the REBASE flat file. |
static java.lang.String |
REBASE_TAG_COMM
REBASE_TAG_COMM the REBASE tag containing the
commercial suppliers. |
static java.lang.String |
REBASE_TAG_ISZR
REBASE_TAG_ISZR the REBASE tag containing the
enzyme isoschizomers. |
static java.lang.String |
REBASE_TAG_METH
REBASE_TAG_METH the REBASE tag containing the
methylation site. |
static java.lang.String |
REBASE_TAG_NAME
REBASE_TAG_NAME the REBASE tag containing the
enzyme name. |
static java.lang.String |
REBASE_TAG_ORGN
REBASE_TAG_ORGN the REBASE tag containing the
organism. |
static java.lang.String |
REBASE_TAG_REFS
REBASE_TAG_REFS the REBASE tag containing the
references. |
static java.lang.String |
REBASE_TAG_SITE
REBASE_TAG_SITE the REBASE tag containing the
enzyme site. |
static java.lang.String |
REBASE_TAG_SRCE
REBASE_TAG_SRCE the REBASE tag containing the
source. |
Method Summary | |
static java.util.Set |
getAllEnzymes()
getAllEnzymes returns an unmodifable set of all
available enzymes. |
static Annotation |
getAnnotation(RestrictionEnzyme enzyme)
getAnnotation returns an immutable, static
annotation describing the enzyme. |
static RestrictionEnzyme |
getEnzyme(java.lang.String name)
getEnzyme returns an enzyme by name. |
static java.util.Set |
getIsoschizomers(java.lang.String name)
getIsoschizomers returns an unmodifable set of the
isoschizomers of this enzyme. |
static java.util.Set |
getNCutters(int n)
getNCutters returns an unmodifable set of all
enzymes with a cut site of size n. |
static java.util.regex.Pattern[] |
getPatterns(RestrictionEnzyme enzyme)
getPatterns returns two Pattern
objects for an enzyme, one matches the forward strand and one
the reverse. |
static void |
register(RestrictionEnzyme enzyme,
java.util.Set isoschizomers)
register regisiters a new
RestrictionEnzyme with the manager. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
public static final java.lang.String REBASE_DATA_KEY
REBASE_DATA_KEY
the ResourceBundle key which
specifies the location of the REBASE flat file.
public static final java.lang.String REBASE_TAG_NAME
REBASE_TAG_NAME
the REBASE tag containing the
enzyme name.
public static final java.lang.String REBASE_TAG_ISZR
REBASE_TAG_ISZR
the REBASE tag containing the
enzyme isoschizomers.
public static final java.lang.String REBASE_TAG_SITE
REBASE_TAG_SITE
the REBASE tag containing the
enzyme site.
public static final java.lang.String REBASE_TAG_METH
REBASE_TAG_METH
the REBASE tag containing the
methylation site.
public static final java.lang.String REBASE_TAG_ORGN
REBASE_TAG_ORGN
the REBASE tag containing the
organism.
public static final java.lang.String REBASE_TAG_SRCE
REBASE_TAG_SRCE
the REBASE tag containing the
source.
public static final java.lang.String REBASE_TAG_COMM
REBASE_TAG_COMM
the REBASE tag containing the
commercial suppliers.
public static final java.lang.String REBASE_TAG_REFS
REBASE_TAG_REFS
the REBASE tag containing the
references.
Method Detail |
public static java.util.Set getAllEnzymes()
getAllEnzymes
returns an unmodifable set of all
available enzymes.
Set
of RestrictionEnzyme
s.public static RestrictionEnzyme getEnzyme(java.lang.String name)
getEnzyme
returns an enzyme by name.
name
- a String
such as EcoRI, case
sensitive.
RestrictionEnzyme
.public static java.util.Set getIsoschizomers(java.lang.String name)
getIsoschizomers
returns an unmodifable set of the
isoschizomers of this enzyme.
name
- a String
such as EcoRI, case
sensitive.
Set
of RestrictionEnzyme
s.public static java.util.Set getNCutters(int n)
getNCutters
returns an unmodifable set of all
enzymes with a cut site of size n.
n
- an int
cut site size.
Set
of RestrictionEnzyme
s.public static java.util.regex.Pattern[] getPatterns(RestrictionEnzyme enzyme)
getPatterns
returns two Pattern
objects for an enzyme, one matches the forward strand and one
the reverse. This enables searching of both strands of a
sequence without reverse-complementing it. As
Pattern
objects are thread-safe these may be used
for all searches.
enzyme
- a RestrictionEnzyme
.
Pattern []
array with the forward strand
Pattern
at index 0 and the reverse at index 1.public static Annotation getAnnotation(RestrictionEnzyme enzyme)
getAnnotation
returns an immutable, static
annotation describing the enzyme. This is suitable for adding
to Feature
s which represent restriction sites. The
annotation produced currently contains one key "dbxref" in line
with the GenBank/EMBL qualifier for the "misc_binding" feature
key. The key has a corresponding value "REBASE:<enzyme
name>".
enzyme
- a RestrictionEnzyme
.
Annotation
.public static void register(RestrictionEnzyme enzyme, java.util.Set isoschizomers)
register
regisiters a new
RestrictionEnzyme
with the manager. It does not
check that the isoschizomers are known to the manager. If there
are custom isoschizomers in the Set
, they should
be also be registered.
enzyme
- a RestrictionEnzyme
to register.isoschizomers
- a Set
of
RestrictionEnzyme
s which are isoschizomers.
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