com.compomics.util.experiment.biology

Class Enzyme

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Enzyme

All Implemented Interfaces:

Serializable, Cloneable

public class Enzyme
extends ExperimentObject

This class models an enzyme.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Enzyme(int id, String name, String aminoAcidBefore, String restrictionBefore, String aminoAcidAfter, String restrictionAfter) Constructor for an Enzyme.
Enzyme(int id, String name, String aminoAcidBefore, String restrictionBefore, String aminoAcidAfter, String restrictionAfter, Boolean isSemiSpecific, Boolean isWholeProtein) Constructor for an Enzyme.

Method Summary

Modifier and Type	Method and Description
ArrayList<String>	digest(String sequence, int nMissedCleavages, int nMin, int nMax) Digests a protein sequence in a list of expected peptide sequences.
boolean	equals(Enzyme otherEnzyme) Returns true of the two enzymes are identical.
ArrayList<Character>	getAminoAcidAfter() Getter for the amino acids potentially following the cleavage.
ArrayList<Character>	getAminoAcidBefore() Getter for the amino acids potentially preceding the cleavage.
String	getDescription() Returns the description of the cleavage of this enzyme.
int	getId() Get the enzyme id.
String	getMyriMatchFormat() Get the MyriMatch enzyme format.
String	getName() Get the enzyme name.
int	getNmissedCleavages(String sequence) Returns the number of missed cleavages in an amino acid sequence.
ArrayList<Character>	getRestrictionAfter() Getter for the amino acids restricting when following the cleavage.
ArrayList<Character>	getRestrictionBefore() Getter for the amino acids restricting when preceding the cleavage.
String	getXTandemFormat() Get the X!Tandem enzyme format.
boolean	isCleavageSite(char aaBefore, char aaAfter) Returns a boolean indicating whether the given amino acids represent a cleavage site.
boolean	isCleavageSite(String aaBefore, String aaAfter) Returns a boolean indicating whether the given amino acids represent a cleavage site.
boolean	isSemiSpecific() Returns true if the enzyme is semi-specific.
boolean	isUnspecific() Returns true if the enzyme is unspecific, i.e., cleaves at every residue.
boolean	isWholeProtein() Returns true if the enzyme does not cleave at all, i.e., the whole protein is used.
void	setSemiSpecific(boolean isSemiSpecific) Set if the enzyme is semi-specific.
void	setWholeProtein(boolean isWholeProtein) Set if the enzyme does not cleave at all, i.e., the whole protein is used.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Constructor Detail

Enzyme

public Enzyme(int id,
              String name,
              String aminoAcidBefore,
              String restrictionBefore,
              String aminoAcidAfter,
              String restrictionAfter)

Constructor for an Enzyme.

Parameters:

id - the enzyme id which should be OMSSA compatible.

name - the name of the enzyme

aminoAcidBefore - the amino acids which can be found before the cleavage

restrictionBefore - the amino acids which should not be found before the cleavage

aminoAcidAfter - the amino acids which should be found after the cleavage

restrictionAfter - the amino acids which should not be found after the cleavage

Enzyme

public Enzyme(int id,
              String name,
              String aminoAcidBefore,
              String restrictionBefore,
              String aminoAcidAfter,
              String restrictionAfter,
              Boolean isSemiSpecific,
              Boolean isWholeProtein)

Constructor for an Enzyme.

Parameters:

id - the enzyme id which should be OMSSA compatible.

name - the name of the enzyme

aminoAcidBefore - the amino acids which can be found before the cleavage

restrictionBefore - the amino acids which should not be found before the cleavage

aminoAcidAfter - the amino acids which should be found after the cleavage

restrictionAfter - the amino acids which should not be found after the cleavage

isSemiSpecific - if true, the enzyme is considered as semi-specific, meaning that only one end of the resulting peptide has to be enzymatic

isWholeProtein - if true, the enzyme does not cleave, i.e., the whole protein sequence is used.

Method Detail

isUnspecific

public boolean isUnspecific()

Returns true if the enzyme is unspecific, i.e., cleaves at every residue.

Returns:

true if the enzyme is unspecific

getName

public String getName()

Get the enzyme name.

Returns:

the enzyme name as String

getId

public int getId()

Get the enzyme id.

Returns:

the enzyme number

getXTandemFormat

public String getXTandemFormat()

Get the X!Tandem enzyme format.

Returns:

the enzyme X!Tandem format as String

getMyriMatchFormat

public String getMyriMatchFormat()

Get the MyriMatch enzyme format.

Returns:

the enzyme MyriMatch format as String

getAminoAcidAfter

public ArrayList<Character> getAminoAcidAfter()

Getter for the amino acids potentially following the cleavage.

Returns:

the amino acids potentially following the cleavage

getAminoAcidBefore

public ArrayList<Character> getAminoAcidBefore()

Getter for the amino acids potentially preceding the cleavage.

Returns:

the amino acids potentially preceding the cleavage

getRestrictionAfter

public ArrayList<Character> getRestrictionAfter()

Getter for the amino acids restricting when following the cleavage.

Returns:

the amino acids restricting when following the cleavage

getRestrictionBefore

public ArrayList<Character> getRestrictionBefore()

Getter for the amino acids restricting when preceding the cleavage.

Returns:

the amino acids restricting when preceding the cleavage

isCleavageSite

public boolean isCleavageSite(String aaBefore,
                              String aaAfter)

Returns a boolean indicating whether the given amino acids represent a cleavage site. Trypsin example: (D, E) returns false (R, D) returns true Note: returns false if no cleavage site is implemented.

Parameters:

aaBefore - the amino acid before the cleavage site

aaAfter - the amino acid after the cleavage site

Returns:

true if the amino acid combination can represent a cleavage site

isCleavageSite

public boolean isCleavageSite(char aaBefore,
                              char aaAfter)

Returns a boolean indicating whether the given amino acids represent a cleavage site. Trypsin example: (D, E) returns false (R, D) returns true Note: returns false if no cleavage site is implemented.

Parameters:

aaBefore - the amino acid before the cleavage site

aaAfter - the amino acid after the cleavage site

Returns:

true if the amino acid combination can represent a cleavage site

getNmissedCleavages

public int getNmissedCleavages(String sequence)

Returns the number of missed cleavages in an amino acid sequence.

Parameters:

sequence - the amino acid sequence as a string.

Returns:

the number of missed cleavages

digest

public ArrayList<String> digest(String sequence,
                                int nMissedCleavages,
                                int nMin,
                                int nMax)

Digests a protein sequence in a list of expected peptide sequences.

Parameters:

sequence - the protein sequence

nMissedCleavages - the maximum number of missed cleavages

nMin - the minimal size for a peptide

nMax - the maximal size for a peptide

Returns:

a list of expected peptide sequences

equals

public boolean equals(Enzyme otherEnzyme)

Returns true of the two enzymes are identical.

Parameters:

otherEnzyme - the enzyme to compare against.

Returns:

true of the two enzymes are identical

setSemiSpecific

public void setSemiSpecific(boolean isSemiSpecific)

Set if the enzyme is semi-specific.

Parameters:

isSemiSpecific - if the enzyme is semi-specific

isSemiSpecific

public boolean isSemiSpecific()

Returns true if the enzyme is semi-specific.

Returns:

true if the enzyme is semi-specific

setWholeProtein

public void setWholeProtein(boolean isWholeProtein)

Set if the enzyme does not cleave at all, i.e., the whole protein is used.

Parameters:

isWholeProtein - if the enzyme does not cleave at all

isWholeProtein

public boolean isWholeProtein()

Returns true if the enzyme does not cleave at all, i.e., the whole protein is used.

Returns:

true if the enzyme does not cleave at all

getDescription

public String getDescription()

Returns the description of the cleavage of this enzyme.

Returns:

the description of the cleavage of this enzyme