RestrictionEnzymeManager (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.molbio.RestrictionEnzymeManager

```
public final class RestrictionEnzymeManager
extends Object
```
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".

Since 1.5, a format #31 REBASE file can be loaded at anytime using the method loadEnzymeFile and optionally filtered for commercially available enzymes.

Since:

1.3

Author:

Keith James, George Waldon

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`REBASE_DATA_KEY` `REBASE_DATA_KEY` the ResourceBundle key which specifies the location of the REBASE flat file.
`static String`	`REBASE_TAG_COMM` `REBASE_TAG_COMM` the REBASE tag containing the commercial suppliers.
`static String`	`REBASE_TAG_ISZR` `REBASE_TAG_ISZR` the REBASE tag containing the enzyme isoschizomers.
`static String`	`REBASE_TAG_METH` `REBASE_TAG_METH` the REBASE tag containing the methylation site.
`static String`	`REBASE_TAG_NAME` `REBASE_TAG_NAME` the REBASE tag containing the enzyme name.
`static String`	`REBASE_TAG_ORGN` `REBASE_TAG_ORGN` the REBASE tag containing the organism.
`static String`	`REBASE_TAG_REFS` `REBASE_TAG_REFS` the REBASE tag containing the references.
`static String`	`REBASE_TAG_SITE` `REBASE_TAG_SITE` the REBASE tag containing the enzyme site.
`static String`	`REBASE_TAG_SRCE` `REBASE_TAG_SRCE` the REBASE tag containing the source.

Method Summary

Methods
Modifier and Type	Method and Description
`static 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(String name)` `getEnzyme` returns an enzyme by name.
`static Set`	`getIsoschizomers(String name)` `getIsoschizomers` returns an unmodifable set of the isoschizomers of this enzyme.
`static Set`	`getNCutters(int n)` `getNCutters` returns an unmodifable set of all enzymes with a cut site of size n.
`static Pattern[]`	`getPatterns(RestrictionEnzyme enzyme)` `getPatterns` returns two `Pattern` objects for an enzyme, one matches the forward strand and one the reverse.
`static String`	`getRecognitionSequence(String name)` `getRecognitionSequence` returns a string that describes the recognition site of this enzyme.
`static String`	`getSuppliers(RestrictionEnzyme enzyme)` `getSuppliers` returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.
`static void`	`loadEnzymeFile(InputStream is, boolean commercialOnly)` `loadEnzymeFile` loads a new REBASE file (or any file using REBASE format #31).
`static void`	`register(RestrictionEnzyme enzyme, 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
  - REBASE_DATA_KEY
```
public static final String REBASE_DATA_KEY
```
    REBASE_DATA_KEY the ResourceBundle key which specifies the location of the REBASE flat file.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_NAME
```
public static final String REBASE_TAG_NAME
```
    REBASE_TAG_NAME the REBASE tag containing the enzyme name.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_ISZR
```
public static final String REBASE_TAG_ISZR
```
    REBASE_TAG_ISZR the REBASE tag containing the enzyme isoschizomers.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_SITE
```
public static final String REBASE_TAG_SITE
```
    REBASE_TAG_SITE the REBASE tag containing the enzyme site.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_METH
```
public static final String REBASE_TAG_METH
```
    REBASE_TAG_METH the REBASE tag containing the methylation site.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_ORGN
```
public static final String REBASE_TAG_ORGN
```
    REBASE_TAG_ORGN the REBASE tag containing the organism.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_SRCE
```
public static final String REBASE_TAG_SRCE
```
    REBASE_TAG_SRCE the REBASE tag containing the source.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_COMM
```
public static final String REBASE_TAG_COMM
```
    REBASE_TAG_COMM the REBASE tag containing the commercial suppliers.
    
    See Also:
    Constant Field Values
  - REBASE_TAG_REFS
```
public static final String REBASE_TAG_REFS
```
    REBASE_TAG_REFS the REBASE tag containing the references.
    
    See Also:
    Constant Field Values
- Method Detail
  - loadEnzymeFile
```
public static void loadEnzymeFile(InputStream is,
                  boolean commercialOnly)
```
    loadEnzymeFile loads a new REBASE file (or any file using REBASE format #31).
    
    Parameters:
    is - an InputStream over the file to load.
    commercialOnly - indicates whether or not only commercially available enzymes are loaded.
    Since:
    
    1.5
  - getAllEnzymes
```
public static Set getAllEnzymes()
```
    getAllEnzymes returns an unmodifable set of all available enzymes.
    
    Returns:
    a Set of RestrictionEnzymes.
  - getEnzyme
```
public static RestrictionEnzyme getEnzyme(String name)
```
    getEnzyme returns an enzyme by name.
    
    Parameters:
    name - a String such as EcoRI, case sensitive.
    
    Returns:
    a RestrictionEnzyme.
  - getIsoschizomers
```
public static Set getIsoschizomers(String name)
```
    getIsoschizomers returns an unmodifable set of the isoschizomers of this enzyme.
    
    Parameters:
    name - a String such as EcoRI, case sensitive.
    
    Returns:
    a Set of RestrictionEnzymes.
  - getRecognitionSequence
```
public static String getRecognitionSequence(String name)
```
    getRecognitionSequence returns a string that describes the recognition site of this enzyme. It corresponds to the field <3> of the REBASE file.
    
    Parameters:
    name - a String such as EcoRI, case sensitive.
    
    Returns:
    a String describing the recognition sequence, e.g. "G^AATTC" for EcoRI.
    Since:
    
    1.5
  - getNCutters
```
public static Set getNCutters(int n)
```
    getNCutters returns an unmodifable set of all enzymes with a cut site of size n.
    
    Parameters:
    n - an int cut site size.
    
    Returns:
    a Set of RestrictionEnzymes.
  - getPatterns
```
public static 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.
    
    Parameters:
    enzyme - a RestrictionEnzyme.
    
    Returns:
    a Pattern [] array with the forward strand Pattern at index 0 and the reverse at index 1.
  - getAnnotation
```
public static Annotation getAnnotation(RestrictionEnzyme enzyme)
```
    getAnnotation returns an immutable, static annotation describing the enzyme. This is suitable for adding to Features 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>".
    
    Parameters:
    enzyme - a RestrictionEnzyme.
    
    Returns:
    an Annotation.
  - getSuppliers
```
public static String getSuppliers(RestrictionEnzyme enzyme)
```
    getSuppliers returns a string describing the suppliers of this enzyme according to REBASE encoding for commercial sources or an empty String if the enzyme is not commecially available.
    REBASE #31 version 604 code:
    
    A GE Healthcare (8/05)
    B Invitrogen Corporation(8/05)
    C Minotech Biotechnology (9/05)
    E Stratagene (9/05)
    F Fermentas International Inc. (2/06)
    G Qbiogene (9/05)
    H American Allied Biochemical, Inc. (9/05)
    I SibEnzyme Ltd. (2/06)
    J Nippon Gene Co., Ltd. (8/05)
    K Takara Bio Inc. (9/05)
    M Roche Applied Science (8/05)
    N New England Biolabs (2/06)
    O Toyobo Biochemicals (9/05)
    Q Molecular Biology Resources (8/05)
    R Promega Corporation (9/05)
    S Sigma Chemical Corporation (9/05)
    U Bangalore Genei (9/05)
    V Vivantis Technologies (1/06)
    X EURx Ltd. (9/05)
    Y CinnaGen Inc. (9/05)
    
    Parameters:
    enzyme - a RestrictionEnzyme.
    
    Returns:
    a String.
    Since:
    
    1.5
  - register
```
public static void register(RestrictionEnzyme enzyme,
            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.
    
    Parameters:
    enzyme - a RestrictionEnzyme to register.
    isoschizomers - a Set of RestrictionEnzymes which are isoschizomers.

Class RestrictionEnzymeManager

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

REBASE_DATA_KEY

REBASE_TAG_NAME

REBASE_TAG_ISZR

REBASE_TAG_SITE

REBASE_TAG_METH

REBASE_TAG_ORGN

REBASE_TAG_SRCE

REBASE_TAG_COMM

REBASE_TAG_REFS

Method Detail

loadEnzymeFile

getAllEnzymes

getEnzyme

getIsoschizomers

getRecognitionSequence

getNCutters

getPatterns

getAnnotation

getSuppliers

register