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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.
Constructor Summary | |
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Enzyme(int id,
String name,
String aminoAcidBefore,
String restrictionBefore,
String aminoAcidAfter,
String restrictionAfter)
Constructor for an Enzyme. |
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Enzyme(int id,
String name,
String aminoAcidBefore,
String restrictionBefore,
String aminoAcidAfter,
String restrictionAfter,
Boolean isSemiSpecific)
Constructor for an Enzyme. |
Method Summary | |
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ArrayList<String> |
digest(String sequence,
int nMissedCleavages,
int nMin,
int nMax)
Digests a protein sequence in a list of expected peptide sequences. |
boolean |
enzymeCleaves()
Deprecated. use isSemiSpecific instead |
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. |
int |
getId()
Get the enzyme id. |
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)
Deprecated. use the isCleavageSite method using chars as input instead |
boolean |
isSemiSpecific()
Returns true if the enzyme is semi-specific. |
void |
setSemiSpecific(boolean isSemiSpecific)
Set if the enzyme is semi-specific. |
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, String name, String aminoAcidBefore, String restrictionBefore, String aminoAcidAfter, 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 cleavagepublic Enzyme(int id, String name, String aminoAcidBefore, String restrictionBefore, String aminoAcidAfter, String restrictionAfter, Boolean isSemiSpecific)
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 cleavageisSemiSpecific
- if true, the enzyme is considered as semi-specific,
meaning that only one end of the resulting peptide has to be enzymaticMethod Detail |
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public String getName()
public int getId()
public String getXTandemFormat()
public ArrayList<Character> getAminoAcidAfter()
public ArrayList<Character> getAminoAcidBefore()
public ArrayList<Character> getRestrictionAfter()
public ArrayList<Character> getRestrictionBefore()
public boolean enzymeCleaves()
public boolean isCleavageSite(String aaBefore, String aaAfter)
aaBefore
- the amino acid before the cleavage siteaaAfter
- the amino acid after the cleavage site
public boolean isCleavageSite(char aaBefore, char aaAfter)
aaBefore
- the amino acid before the cleavage siteaaAfter
- the amino acid after the cleavage site
public int getNmissedCleavages(String sequence)
sequence
- the amino acid sequence as a string.
public ArrayList<String> digest(String sequence, int nMissedCleavages, int nMin, int nMax)
sequence
- the protein sequencenMissedCleavages
- the maximum number of missed cleavagesnMin
- the minimal size for a peptidenMax
- the maximal size for a peptide
public boolean equals(Enzyme otherEnzyme)
otherEnzyme
- the enzyme to compare against.
public void setSemiSpecific(boolean isSemiSpecific)
isSemiSpecific
- if the enzyme is semi-specificpublic boolean isSemiSpecific()
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