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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Enzyme
public class Enzyme
This class models an enzyme. Created by IntelliJ IDEA. User: Marc Date: Aug 23, 2010 Time: 1:44:12 PM
Constructor Summary | |
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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 | |
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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. |
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! |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Enzyme(int id, java.lang.String name, java.lang.String aminoAcidBefore, java.lang.String restrictionBefore, java.lang.String aminoAcidAfter, java.lang.String restrictionAfter)
id
- the enzyme id which should be OMSSA compatible.name
- the name of the enzymeaminoAcidBefore
- the amino-acids which can be found before the cleavagerestrictionBefore
- the amino-acids which should not be found before the cleavageaminoAcidAfter
- the amino-acids which should be found after the cleavagerestrictionAfter
- the amino-acids which should not be found after the cleavageMethod Detail |
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public java.lang.String getName()
public int getId()
public java.lang.String getXTandemFormat()
public java.util.ArrayList<java.lang.Character> getAminoAcidAfter()
public java.util.ArrayList<java.lang.Character> getAminoAcidBefore()
public java.util.ArrayList<java.lang.Character> getRestrictionAfter()
public java.util.ArrayList<java.lang.Character> getRestrictionBefore()
public java.util.ArrayList<java.lang.String> digest(java.lang.String sequence, int nMissedCleavages, int nMin, int nMax)
sequence
- the protein sequencenMissedCleavages
- the allowed number of missed cleavagesnMin
- the minimal size for a peptidenMax
- the maximal size for a peptide
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