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

All Implemented Interfaces:

Serializable
```
public class RestrictionEnzyme
extends Object
implements Serializable
```
RestrictionEnzyme represents a restriction enzyme according to the REBASE standard. The cut positions are indicated relative to the 5' end of the recognition site and occur downstream of the given residue. Note that some enzymes cut in more than one position and that cut positions may occur outside the recognition site.

Since:

1.3

Author:

Keith James, George Waldon

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`BLUNT`	`BLUNT` the end type created by enzymes which leave a blunt end.
`static int`	`CUT_COMPOUND`	`CUT_COMPOUND` a cut type where the enzyme cuts in two positions relative to the recognition site.
`static int`	`CUT_SIMPLE`	`CUT_SIMPLE` a cut type where the enzyme cuts in one position relative to the recognition site.
`protected int`	`cutType`
`protected int[]`	`dsCutPositions`
`protected String`	`forwardRegex`
`protected String`	`name`
`static int`	`OVERHANG_3PRIME`	`OVERHANG_3PRIME` the sticky end type created by enzymes which leave a 3' overhang (e.g. a stretch of single-stranded DNA with a free 3' end).
`static int`	`OVERHANG_5PRIME`	`OVERHANG_5PRIME` the sticky end type created by enzymes which leave a 5' overhang (e.g. a stretch of single-stranded DNA with a free 5' end).
`protected String`	`reverseRegex`
`protected SymbolList`	`site`
`protected int[]`	`usCutPositions`

Constructor Summary

Constructors
Constructor	Description
`RestrictionEnzyme(String name, SymbolList site, int dsForward, int dsReverse)`	Creates a new `RestrictionEnzyme` which cuts within or downstream of the recognition site.
`RestrictionEnzyme(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse)`	Creates a new `RestrictionEnzyme` of the unusual type which cuts both upstream and downstream of its recognition site.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`equals(Object o)`
`double`	`getCuttingSize()`	The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence.
`int`	`getCutType()`	`getCutType` returns the type of cut produced by the enzyme.
`int[]`	`getDownstreamCut()`	`getDownstreamCut` returns the cut site within or downstream of the recognition site.
`int`	`getDownstreamEndType()`	`getDownstreamEndType` returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
`String`	`getForwardRegex()`	`getForwardRegex` returns a regular expression which matches the forward strand of the recognition site.
`String`	`getName()`	`getName` returns the enzyme name.
`RestrictionEnzyme`	`getPrototype()`	The prototype is a `RestrictionEnzyme` that represents a set of isoshizomers.
`SymbolList`	`getRecognitionSite()`	`getRecognitionSite` returns the forward strand of the recognition site.
`String`	`getReverseRegex()`	`getReverseRegex` returns a regular expression which matches the reverse strand of the recognition site.
`int[]`	`getUpstreamCut()`	`getUpstreamCut` returns the cut site upstream of the recognition site.
`int`	`getUpstreamEndType()`	`getUpstreamEndType` returns the double-stranded end type produced by the secondary (upstream) cut.
`int`	`hashCode()`
`boolean`	`isPalindromic()`	`isPalindromic` returns true if the recognition site is palindromic.
`boolean`	`isPrototype()`
`void`	`setProtype(RestrictionEnzyme proto)`	Set the prototype of this `RestrictionEnzyme`.
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - CUT_SIMPLE
```
public static final int CUT_SIMPLE
```
    CUT_SIMPLE a cut type where the enzyme cuts in one position relative to the recognition site. This covers the vast majority of cases.
    
    See Also:
    
    Constant Field Values
  - CUT_COMPOUND
```
public static final int CUT_COMPOUND
```
    CUT_COMPOUND a cut type where the enzyme cuts in two positions relative to the recognition site.
    
    See Also:
    
    Constant Field Values
  - OVERHANG_5PRIME
```
public static final int OVERHANG_5PRIME
```
    OVERHANG_5PRIME the sticky end type created by enzymes which leave a 5' overhang (e.g. a stretch of single-stranded DNA with a free 5' end).
    
    See Also:
    
    Constant Field Values
  - OVERHANG_3PRIME
```
public static final int OVERHANG_3PRIME
```
    OVERHANG_3PRIME the sticky end type created by enzymes which leave a 3' overhang (e.g. a stretch of single-stranded DNA with a free 3' end).
    
    See Also:
    
    Constant Field Values
  - BLUNT
```
public static final int BLUNT
```
    BLUNT the end type created by enzymes which leave a blunt end.
    
    See Also:
    
    Constant Field Values
  - name
```
protected String name
```
  - site
```
protected SymbolList site
```
  - cutType
```
protected int cutType
```
  - dsCutPositions
```
protected int[] dsCutPositions
```
  - usCutPositions
```
protected int[] usCutPositions
```
  - forwardRegex
```
protected String forwardRegex
```
  - reverseRegex
```
protected String reverseRegex
```
- Constructor Detail
  - RestrictionEnzyme
```
public RestrictionEnzyme(String name,
                         SymbolList site,
                         int dsForward,
                         int dsReverse)
                  throws IllegalAlphabetException
```
    Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site. The cut position indices are always in the same coordinate space as the recognition site. RestrictionEnzymes are immutable.
    
    Parameters:
    
    name - a String such as EcoRI.
    
    site - a SymbolList recognition site.
    
    dsForward - an int index in the forward strand (the strand conventionally written 5'-3') of the recognition site at which the cut occurs. The cut occurs between this base and the following one.
    
    dsReverse - an int index in the reverse strand (the strand conventionally written 3'-5') of the recognition site at which the cut occurs. The cut occurs between this base and the following one.
    
    Throws:
    
    IllegalAlphabetException - if an error occurs.
  - RestrictionEnzyme
```
public RestrictionEnzyme(String name,
                         SymbolList site,
                         int usForward,
                         int usReverse,
                         int dsForward,
                         int dsReverse)
                  throws IllegalAlphabetException
```
    Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site. The cut position indices are always in the same coordinate space as the recognition site.
    
    Parameters:
    
    name - a String such as Bsp24I.
    
    site - a SymbolList recognition site.
    
    usForward - an int index in the forward strand (the strand conventionally written 5'-3' upstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.
    
    usReverse - an int index in the reverse strand (the strand conventionally written 3'-5) upstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.
    
    dsForward - an int index in the forward strand (the strand conventionally written 5'-3') downstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.
    
    dsReverse - an int index in the reverse strand (the strand conventionally written 3'-5') downstream of the recognition site at which the cut occurs. The cut occurs between this base and the following one.
    
    Throws:
    
    IllegalAlphabetException - if an error occurs.
- Method Detail
  - getName
```
public String getName()
```
    getName returns the enzyme name.
    
    Returns:
    
    a String.
  - getRecognitionSite
```
public SymbolList getRecognitionSite()
```
    getRecognitionSite returns the forward strand of the recognition site.
    
    Returns:
    
    a SymbolList.
  - getForwardRegex
```
public String getForwardRegex()
```
    getForwardRegex returns a regular expression which matches the forward strand of the recognition site.
    
    Returns:
    
    a String.
  - getReverseRegex
```
public String getReverseRegex()
```
    getReverseRegex returns a regular expression which matches the reverse strand of the recognition site.
    
    Returns:
    
    a String.
  - isPalindromic
```
public boolean isPalindromic()
```
    isPalindromic returns true if the recognition site is palindromic.
    
    Returns:
    
    a boolean.
  - getCutType
```
public int getCutType()
```
    getCutType returns the type of cut produced by the enzyme. This will be one of either RestrictionEnzyme.CUT_SIMPLE (where it cuts in one position relative to the recognition site i.e. the vast majority of cases) or RestrictionEnzyme.CUT_COMPOUND (where it cuts in two positions).
    
    Returns:
    
    an int.
  - getDownstreamCut
```
public int[] getDownstreamCut()
```
    getDownstreamCut returns the cut site within or downstream of the recognition site.
    
    Returns:
    
    an int [] array with the position in the 5'-strand at index 0 and the 3'-strand at index 1.
  - getUpstreamCut
```
public int[] getUpstreamCut()
                     throws BioException
```
    getUpstreamCut returns the cut site upstream of the recognition site.
    
    Returns:
    
    an int [] array with the position in the 5'-strand at index 0 and the 3'-strand at index 1. For example, Bsp24I will return -8 and -13: 5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3' 3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5'
    
    Throws:
    
    BioException - if the enzyme does not cleave on both sides of its recognition site.
  - getDownstreamEndType
```
public int getDownstreamEndType()
```
    getDownstreamEndType returns the double-stranded end type produced by the primary (intra-site or downstream) cut.
    
    Returns:
    
    an int equal to one of the constant fields OVERHANG_5PRIME, OVERHANG_3PRIME or BLUNT.
  - getUpstreamEndType
```
public int getUpstreamEndType()
                       throws BioException
```
    getUpstreamEndType returns the double-stranded end type produced by the secondary (upstream) cut.
    
    Returns:
    
    an int equal to one of the constant fields OVERHANG_5PRIME, OVERHANG_3PRIME or BLUNT.
    
    Throws:
    
    BioException - if the enzyme does not cleave on both sides of its recognition site.
  - setProtype
```
public void setProtype(RestrictionEnzyme proto)
```
    Set the prototype of this RestrictionEnzyme.
    
    Parameters:
    
    proto - an isoschizomer of this enzyme.
  - getPrototype
```
public RestrictionEnzyme getPrototype()
```
    The prototype is a RestrictionEnzyme that represents a set of isoshizomers. The choice of the representative/prototype is arbitrary; there is one and only one prototype per set of isoschizomers.
    
    Returns:
    
    A representative isoschisomer or null if prototypes are not defined.
  - isPrototype
```
public boolean isPrototype()
```
  - getCuttingSize
```
public double getCuttingSize()
```
    The cutting size of a restriction enzyme is defined has the number of nucleotides that are directly involved in the recognition sequence. The size is ponderated as follow: 1 for a single nucleotide, 1/2 for a degeneracy of 2, 1/4 for a degeneracy of 3, and 0 for any N nucleotides.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class RestrictionEnzyme

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CUT_SIMPLE

CUT_COMPOUND

OVERHANG_5PRIME

OVERHANG_3PRIME

BLUNT

name

site

cutType

dsCutPositions

usCutPositions

forwardRegex

reverseRegex

Constructor Detail

RestrictionEnzyme

RestrictionEnzyme

Method Detail

getName

getRecognitionSite

getForwardRegex

getReverseRegex

isPalindromic

getCutType

getDownstreamCut

getUpstreamCut

getDownstreamEndType

getUpstreamEndType

setProtype

getPrototype

isPrototype

getCuttingSize

hashCode

equals

toString