com.compomics.util.protein

Class RegExEnzyme

java.lang.Object

com.compomics.util.protein.Enzyme

com.compomics.util.protein.RegExEnzyme

All Implemented Interfaces:

Cloneable

public class RegExEnzyme
extends Enzyme

This class implements the functionality of an Enzyme by simulating digestion based on a regular expression.

Since:

2.9

Author:

Florian Reisinger

Field Summary

Fields inherited from class com.compomics.util.protein.Enzyme

C_TERM_ENZYMATIC, CTERM, ENTIRELY_NOT_ENZYMATIC, FULLY_ENZYMATIC, iCleavables, iCleavage, iMiscleavages, iPosition, iRestrict, iRestrictors, iTitle, N_TERM_ENZYMATIC, NTERM

Constructor Summary

Constructors

Constructor and Description
RegExEnzyme(String aTitle, String aCleavage, String aRestrict, String aPosition) Create a new RegExEnzyme.
RegExEnzyme(String aTitle, String aCleavage, String aRestrict, String aPosition, int aMiscleavages) Create a new RegExEnzyme.

Method Summary

Modifier and Type	Method and Description
Protein[]	cleave(Protein aProtein) This method is the focus of the Enzyme instance.
Object	clone() This method returns a deep copy of the current Enzyme.
char[]	getCleavage() Simple getter for the cleavagable residues of the Enzyme.
int	isEnzymaticProduct(String aParentSequence, int aStart, int aEnd) This method reports on the possibility that the presented subsequence (represented by the start and end location in the parent) is the result of enzymatic activity.
int	isEnzymaticProduct(String aParentSequence, String aSubSequence) This method reports on the possibility that the presented subsequence is the result of enzymatic activity.
void	setCleavage(char[] aCleavage) This method allows the caller to specify the cleavable residues.
void	setCleavage(String aCleavage) This method can be used to set the cleavage pattern for this RegExEnzyme.
String	toString() This method generates a String representation of the Enzyme, which is useful for displaying as useful information for the user or during testing/debugging.
String	toString(String aPrepend) This method generates a String representation of the Enzyme, which is useful for displaying as useful information for the user or during testing/debugging.

Methods inherited from class com.compomics.util.protein.Enzyme

cleave, getMiscleavages, getPosition, getRestrict, getTitle, setMiscleavages, setPosition, setRestrict, setRestrict, setTitle

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

RegExEnzyme

public RegExEnzyme(String aTitle,
                   String aCleavage,
                   String aRestrict,
                   String aPosition)

Create a new RegExEnzyme.

Parameters:

aTitle - the title

aCleavage - the cleavage site

aRestrict - the restricting amino acids

aPosition - the position

RegExEnzyme

public RegExEnzyme(String aTitle,
                   String aCleavage,
                   String aRestrict,
                   String aPosition,
                   int aMiscleavages)

Create a new RegExEnzyme.

Parameters:

aTitle - the title

aCleavage - the cleavage site

aRestrict - the restricting amino acids

aPosition - the position

aMiscleavages - max number of miscleavages

Method Detail

setCleavage

public void setCleavage(String aCleavage)

This method can be used to set the cleavage pattern for this RegExEnzyme. The pattern is used by the enzyme to find the cleavage sits, where the last residue matched by the pattern defines the cleavage site. (e.g. in case of C-terminal cleavage, the enzyme cuts right after the match of the pattern, and in case of N-terminal cleavage, the enzyme cuts just before the last residue matching the pattern)

Overrides:

setCleavage in class Enzyme

Parameters:

aCleavage - a String representing the pattern for the cleavage site.

Throws:

PatternSyntaxException - if the provided string could not be compiled as regular expression.

setCleavage

public void setCleavage(char[] aCleavage)

Description copied from class: Enzyme

This method allows the caller to specify the cleavable residues.

Overrides:

setCleavage in class Enzyme

Parameters:

aCleavage - char[] with the cleavable residues (in UPPER CASE!).

getCleavage

public char[] getCleavage()

Description copied from class: Enzyme

Simple getter for the cleavagable residues of the Enzyme.

Overrides:

getCleavage in class Enzyme

Returns:

char[] with the cleavable residues.

toString

public String toString()

Description copied from class: Enzyme

This method generates a String representation of the Enzyme, which is useful for displaying as useful information for the user or during testing/debugging.

Overrides:

toString in class Enzyme

Returns:

String with a textual description of this Enzyme.

toString

public String toString(String aPrepend)

Description copied from class: Enzyme

This method generates a String representation of the Enzyme, which is useful for displaying as useful information for the user or during testing/debugging. It takes a parameter String that is prepended to each line.

Overrides:

toString in class Enzyme

Parameters:

aPrepend - String to prepend to each outputted line.

Returns:

String with a textual description of this Enzyme.

clone

public Object clone()

Description copied from class: Enzyme

This method returns a deep copy of the current Enzyme.

Overrides:

clone in class Enzyme

Returns:

Object Enzyme instance that is a deep copy of the current Enzyme.

isEnzymaticProduct

public int isEnzymaticProduct(String aParentSequence,
                              String aSubSequence)

Description copied from class: Enzyme

This method reports on the possibility that the presented subsequence is the result of enzymatic activity. Note that using a substring, only the FIRST (starting from the N-terminus) occurrence of the subsequence in the parent String will be considered! If multiple occurrences are possible, use the overloaded method that takes indices. Returning int values can be checked against public static final vars on this class.

Overrides:

isEnzymaticProduct in class Enzyme

Parameters:

aParentSequence - String with the parent sequence

aSubSequence - String with the subsequence

Returns:

int with the coded possibility (1 = Full enzymatic product, 2 = N-terminal half enzymatic product, 3 = C-terminal half enzymatic product and 4 = Entirely not an enzymatic product.

isEnzymaticProduct

public int isEnzymaticProduct(String aParentSequence,
                              int aStart,
                              int aEnd)

Description copied from class: Enzyme

This method reports on the possibility that the presented subsequence (represented by the start and end location in the parent) is the result of enzymatic activity. Returning int values can be checked against public static final vars on this class.

Overrides:

isEnzymaticProduct in class Enzyme

Parameters:

aParentSequence - String with the parent sequence

aStart - int with the start of the subsequence relative to the parent (first residue is '1').

aEnd - int with the end of the subsequence relative to the parent

Returns:

int with the coded possibility (1 = Full enzymatic product, 2 = N-terminal half enzymatic product, 3 = C-terminal half enzymatic product and 4 = Entirely not an enzymatic product.

cleave

public Protein[] cleave(Protein aProtein)

Description copied from class: Enzyme

This method is the focus of the Enzyme instance. It can perform an in-silico digest of a Protein sequence according to the specifications detailed in the construction or via the setters. Using this methods returns all possible peptides, regardless of length. To only return peptides within certain lengths use the other cleave method.

Overrides:

cleave in class Enzyme

Parameters:

aProtein - Protein instance to cleave.

Returns:

Protein[] with the resultant peptides.