public class Modification extends IdentifiableParamGroup
The modification for PRIDE Model and MZIdentMl model have the following features: - id: Modification identifier - name: Modification Name. - location: Location of the modification within the peptide - position in peptide sequence. - residues: Specification of the residue (amino acid) on which the modification occurs. - Average Mass Delta: Atomic mass delta considering the natural distribution of isotopes in Daltons. - Average MonoIsotopic Mass Delta: Atomic mass delta when assuming only the most common isotope of elements in Daltons. - Modification database where accession is from (used for PRIDE Objects) - Modification database version is (used for PRIDE Objects)
Constructor and Description |
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Modification(ParamGroup params,
String id,
String name,
int location,
List<String> residues,
List<Double> avgMassDelta,
List<Double> monoisotopicMassDelta,
String modDatabase,
String modDatabaseVersion)
Constructor for Modification Objects
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Modification(String id,
String name,
int location,
List<String> residues,
List<Double> avgMassDelta,
List<Double> monoisotopicMassDelta,
String modDatabase,
String modDatabaseVersion)
Constructor for PRIDE Modification Object
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Modifier and Type | Method and Description |
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boolean |
equals(Object o) |
List<Double> |
getAvgMassDelta()
Get Average Mass Delta List
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int |
getLocation()
Get Location of the Modification
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String |
getModDatabase()
Get Modification DataBase Name
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String |
getModDatabaseVersion()
Get Modification DataBase Version
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List<Double> |
getMonoisotopicMassDelta()
Get monoisotopic Mass Delta List
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List<String> |
getResidues()
Get the Amino Acids associated with this modification
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int |
hashCode() |
void |
setAvgMassDelta(List<Double> avgMassDelta)
Get Average Mass Delta List
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void |
setLocation(int location)
Set Location of the Modification
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void |
setModDatabase(String modDatabase)
Set Modification DataBase Name
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void |
setModDatabaseVersion(String modDatabaseVersion)
Set Modification DataBase Version
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void |
setMonoisotopicMassDelta(List<Double> monoisotopicMassDelta)
Set monoisotopic mass delta List
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void |
setResidues(List<String> residues)
Set the Amino Acids associated with this modification
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getId, getName, setId, setName, toString
addCvParam, addCvParams, addUserParam, addUserParams, getCvParams, getUserParams, isEmpty, removeCvParam, removeCvParams, removeUserParam, removeUserParams, setCvParams, setUserParams
public Modification(String id, String name, int location, List<String> residues, List<Double> avgMassDelta, List<Double> monoisotopicMassDelta, String modDatabase, String modDatabaseVersion)
id
- IDname
- Namelocation
- Locationresidues
- List of the possible residues where the modification is presentavgMassDelta
- List of Possible Average Mass DeltamonoisotopicMassDelta
- List of Possible MonoIsotopic Mass DeltamodDatabase
- DataBase NamemodDatabaseVersion
- DataBase Versionpublic Modification(ParamGroup params, String id, String name, int location, List<String> residues, List<Double> avgMassDelta, List<Double> monoisotopicMassDelta, String modDatabase, String modDatabaseVersion)
params
- ParamGroup (CvTerms and User Params)id
- IDname
- Namelocation
- Locationresidues
- List of the possible residues where the modification is presentavgMassDelta
- List of Possible Average Mass DeltamonoisotopicMassDelta
- List of Possible MonoIsotopic Mass DeltamodDatabase
- DataBase NamemodDatabaseVersion
- DataBase Versionpublic int getLocation()
public void setLocation(int location)
location
- Locationpublic List<String> getResidues()
public void setResidues(List<String> residues)
residues
- List of Residues (Amino Acids)public String getModDatabase()
public void setModDatabase(String modDatabase)
modDatabase
- DataBase Namepublic String getModDatabaseVersion()
public void setModDatabaseVersion(String modDatabaseVersion)
modDatabaseVersion
- DataBase Versionpublic List<Double> getAvgMassDelta()
public void setAvgMassDelta(List<Double> avgMassDelta)
avgMassDelta
- Average Mass Delta Listpublic List<Double> getMonoisotopicMassDelta()
public void setMonoisotopicMassDelta(List<Double> monoisotopicMassDelta)
monoisotopicMassDelta
- monoisotopic mass delta Listpublic boolean equals(Object o)
equals
in class IdentifiableParamGroup
public int hashCode()
hashCode
in class IdentifiableParamGroup
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.