public class SlimModification extends Object
Constructor and Description |
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SlimModification(String idPsiMod,
double deltaMass,
int idUnimod,
String psiModDesc,
String shortNamePsiMod,
List<Specificity> specificityCollection)
Constructor of the Slim Modification Class using as a parameters all attributes
of the class.
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Modifier and Type | Method and Description |
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double |
getDeltaMass()
Get the delta Mass of the Modification
|
String |
getIdPsiMod()
Get the PSI-Mod database identifier.
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int |
getIdUnimod()
Get Unimod database identifier.
|
String |
getPsiModDesc()
Get Name in PSI-Mod database
|
String |
getShortNamePsiMod()
Get short name in PSI-Mod database
|
List<Specificity> |
getSpecificityCollection()
Get a collection of possible specificities of the current modification.
|
boolean |
isSpecificity(Specificity.AminoAcid specificity)
Check if a given AminoAcid is part of the specificity of this SlimModification.
|
boolean |
isSpecificity(Specificity.AminoAcid specificity,
double mass,
double difference)
Check if a given AminoAcid is part of the specificity of this SlimModification,
but only perform this check if the delta mass of this SlimModification is with
the specified difference of the specified mass.
|
void |
setDeltaMass(double deltaMass)
Set a delta Mass of the Modification
|
void |
setIdPsiMod(String idPsiMod)
Set the PSI-Mod database identifier.
|
void |
setIdUnimod(int idUnimod)
Set Unimod database identifier.
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void |
setPsiModDesc(String psiModDesc)
Set Name in PSI-Mod database
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void |
setShortNamePsiMod(String shortNamePsiMod)
Set short name in PSI-Mod database
|
void |
setSpecificityCollection(List<Specificity> specificityCollection)
Set a collection of possible specificities of the current modification.
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public SlimModification(String idPsiMod, double deltaMass, int idUnimod, String psiModDesc, String shortNamePsiMod, List<Specificity> specificityCollection)
idPsiMod
- PSI-Mod database identifier.deltaMass
- delta mass of the PSI-MOD modificationidUnimod
- Unimod database identifier.psiModDesc
- Name in PsiModshortNamePsiMod
- short name in PsI Mod.specificityCollection
- a collection of possible specificities of the current modification.public String getIdPsiMod()
public void setIdPsiMod(String idPsiMod)
idPsiMod
- public double getDeltaMass()
public void setDeltaMass(double deltaMass)
deltaMass
- public int getIdUnimod()
public void setIdUnimod(int idUnimod)
idUnimod
- public String getPsiModDesc()
public void setPsiModDesc(String psiModDesc)
psiModDesc
- public String getShortNamePsiMod()
public void setShortNamePsiMod(String shortNamePsiMod)
shortNamePsiMod
- public List<Specificity> getSpecificityCollection()
public void setSpecificityCollection(List<Specificity> specificityCollection)
specificityCollection
- public boolean isSpecificity(Specificity.AminoAcid specificity)
specificity
- the AminoAcid to check the specificity against.public boolean isSpecificity(Specificity.AminoAcid specificity, double mass, double difference)
specificity
- the AminoAcid to check the specificity against.mass
- the mass to compare against.difference
- the difference between the specified mass and this SliModification's delta mass.isSpecificity(uk.ac.ebi.pridemod.model.Specificity.AminoAcid)
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