com.compomics.util.experiment.biology
Class Enzyme

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.Enzyme
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class Enzyme
extends ExperimentObject

This class models an enzyme. Created by IntelliJ IDEA. User: Marc Date: Aug 23, 2010 Time: 1:44:12 PM

See Also:
Serialized Form

Constructor Summary
Enzyme(int id, java.lang.String name, java.lang.String aminoAcidBefore, java.lang.String restrictionBefore, java.lang.String aminoAcidAfter, java.lang.String restrictionAfter)
          Constructor for an Enzyme
 
Method Summary
 java.util.ArrayList<java.lang.String> digest(java.lang.String sequence, int nMissedCleavages, int nMin, int nMax)
          Digests a protein sequence in a list of expected peptide sequences.
 boolean enzymeCleaves()
          Returns a boolean indicating whether a cleavage site was implemented for this enzyme
 java.util.ArrayList<java.lang.Character> getAminoAcidAfter()
          Getter for the amino acids potentially following the cleavage
 java.util.ArrayList<java.lang.Character> getAminoAcidBefore()
          Getter for the amino acids potentially preceding the cleavage
 int getId()
          Get the enzyme id
 java.lang.String getName()
          Get the enzyme name
 java.util.ArrayList<java.lang.Character> getRestrictionAfter()
          Getter for the amino acids restricting when following the cleavage
 java.util.ArrayList<java.lang.Character> getRestrictionBefore()
          Getter for the amino acids restricting when preceding the cleavage
 java.lang.String getXTandemFormat()
          Get the X!Tandem enzyme format
 
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,
              java.lang.String name,
              java.lang.String aminoAcidBefore,
              java.lang.String restrictionBefore,
              java.lang.String aminoAcidAfter,
              java.lang.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
Method Detail

getName

public java.lang.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 java.lang.String getXTandemFormat()
Get the X!Tandem enzyme format

Returns:
The enzyme X!Tandem format as String

getAminoAcidAfter

public java.util.ArrayList<java.lang.Character> getAminoAcidAfter()
Getter for the amino acids potentially following the cleavage

Returns:
the amino acids potentially following the cleavage

getAminoAcidBefore

public java.util.ArrayList<java.lang.Character> getAminoAcidBefore()
Getter for the amino acids potentially preceding the cleavage

Returns:
the amino acids potentially preceding the cleavage

getRestrictionAfter

public java.util.ArrayList<java.lang.Character> getRestrictionAfter()
Getter for the amino acids restricting when following the cleavage

Returns:
the amino acids restricting when following the cleavage

getRestrictionBefore

public java.util.ArrayList<java.lang.Character> getRestrictionBefore()
Getter for the amino acids restricting when preceding the cleavage

Returns:
the amino acids restricting when preceding the cleavage

enzymeCleaves

public boolean enzymeCleaves()
Returns a boolean indicating whether a cleavage site was implemented for this enzyme

Returns:
a boolean indicating whether a cleavage site was implemented for this enzyme

digest

public java.util.ArrayList<java.lang.String> digest(java.lang.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 allowed 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


Copyright © 2013. All Rights Reserved.