public class Modification extends ExperimentObject
NO_KEY
Constructor and Description |
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Modification()
Constructor for the modification.
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Modification(ModificationType modificationType,
String name,
Double mass,
ArrayList<String> residues,
ModificationCategory category)
Simple constructor for a modification.
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Modification(ModificationType modificationType,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm unimodCvTerm,
CvTerm psiModCvTerm,
ModificationCategory category)
Constructor for a reference modification.
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Modification(ModificationType modificationType,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
ModificationCategory category)
Constructor for a reference modification.
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Modifier and Type | Method and Description |
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void |
addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
addReporterIon(ReporterIon reporterIon)
Adds a reporter ion.
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String |
getAmbiguityKey()
Returns the ambiguity key.
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AtomChain |
getAtomChainAdded()
Returns the atom chain added.
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AtomChain |
getAtomChainRemoved()
Returns the atom chain removed.
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ModificationCategory |
getCategory()
Returns the modification category.
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String |
getHtmlTooltip()
Returns information about the modification as an HTML tooltip.
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double |
getMass()
Getter for the mass difference induced by this modification.
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ModificationType |
getModificationType()
Returns the modification type.
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String |
getName()
Getter for the modification name.
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ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the neutral losses possibly encountered with this modification.
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AminoAcidPattern |
getPattern()
Returns the amino acid pattern targeted by this modification.
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CvTerm |
getPsiModCvTerm()
Returns the PSI-MOD CV term associated with this modification.
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ArrayList<ReporterIon> |
getReporterIons()
Returns the reporter ions possibly encountered with this modification.
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double |
getRoundedMass()
Getter for the rounded mass difference induced by this modification.
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double |
getRoundedMass(int numberOfDecimals)
Getter for the rounded mass difference induced by this modification.
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String |
getShortName()
Getter for the short modification name.
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CvTerm |
getUnimodCvTerm()
Returns the Unimod CV term associated with this modification.
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boolean |
isSameAs(Modification anotherModification)
Returns true if the modification is the same as another one.
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boolean |
isSameAtomicComposition(Modification anotherModification)
Returns true if the atomic composition of the modification is the same as
another one.
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boolean |
isSamePattern(Modification anotherModification)
Returns true if the targeted pattern of the modification is the same as
another one.
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boolean |
isStandardSearch()
Indicates whether a modification can be searched with standard search
engines, i.e., true if it targets a single amino acid position, false if
it targets a complex pattern.
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void |
setAtomChainAdded(AtomChain atomChainAdded)
Sets the atom chain added.
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void |
setAtomChainRemoved(AtomChain atomChainRemoved)
Sets the atom chain removed.
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void |
setCategory(ModificationCategory category)
Set the modification category.
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void |
setName(String name)
Sets the modification name.
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void |
setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification.
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void |
setPattern(AminoAcidPattern pattern)
Sets the amino acid pattern targeted by this modification.
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void |
setPsiModCvTerm(CvTerm cvTerm)
Set the PSI-MOD CV term associated with this modification.
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void |
setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification.
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void |
setShortName(String shortName)
Sets the short modification name.
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void |
setUnimodCvTerm(CvTerm cvTerm)
Set the Unimod CV term associated with this modification.
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String |
toString() |
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public Modification()
public Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, ModificationCategory category)
modificationType
- type of modificationname
- name of the modificationshortName
- short name of the modificationatomChainAdded
- atomic composition of the molecule addedatomChainRemoved
- atomic composition of the molecule removedaminoAcidPattern
- residue pattern affected by this modificationcategory
- the modification categorypublic Modification(ModificationType modificationType, String name, String shortName, AtomChain atomChainAdded, AtomChain atomChainRemoved, AminoAcidPattern aminoAcidPattern, CvTerm unimodCvTerm, CvTerm psiModCvTerm, ModificationCategory category)
modificationType
- type of modificationname
- name of the modificationshortName
- short name of the modificationatomChainAdded
- atomic composition of the molecule addedatomChainRemoved
- atomic composition of the molecule removedaminoAcidPattern
- residue pattern affected by this modificationunimodCvTerm
- the Unimod CV term associated with this modification,
null if not setpsiModCvTerm
- the PSI-MOD CV term associated with this
modification, null if not setcategory
- the modification categorypublic Modification(ModificationType modificationType, String name, Double mass, ArrayList<String> residues, ModificationCategory category)
modificationType
- type of modificationname
- name of the modificationmass
- the mass of the modificationresidues
- list of residues possibly targeted by this modificationcategory
- the modification categorypublic ModificationType getModificationType()
public String getName()
public void setName(String name)
name
- the modification namepublic String getShortName()
public void setShortName(String shortName)
shortName
- the modification namepublic double getMass()
public String getAmbiguityKey()
public double getRoundedMass(int numberOfDecimals)
numberOfDecimals
- the number of decimals to round topublic double getRoundedMass()
public AtomChain getAtomChainAdded()
public void setAtomChainAdded(AtomChain atomChainAdded)
atomChainAdded
- the atom chain addedpublic AtomChain getAtomChainRemoved()
public void setAtomChainRemoved(AtomChain atomChainRemoved)
atomChainRemoved
- the atom chain removedpublic boolean isSameAtomicComposition(Modification anotherModification)
anotherModification
- the modification to compare topublic boolean isSamePattern(Modification anotherModification)
anotherModification
- the modification to compare topublic boolean isSameAs(Modification anotherModification)
anotherModification
- another modificationpublic ArrayList<NeutralLoss> getNeutralLosses()
public void setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- the neutral losses possibly encountered with this
modificationpublic void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- the new neutral losspublic ArrayList<ReporterIon> getReporterIons()
public void setReporterIons(ArrayList<ReporterIon> reporterIons)
reporterIons
- the reporter ions possibly encountered with this
modificationpublic void addReporterIon(ReporterIon reporterIon)
reporterIon
- the reporter ion to addpublic AminoAcidPattern getPattern()
public void setPattern(AminoAcidPattern pattern)
pattern
- the amino acid pattern targeted by this modificationpublic boolean isStandardSearch()
public String getHtmlTooltip()
public CvTerm getUnimodCvTerm()
public void setUnimodCvTerm(CvTerm cvTerm)
cvTerm
- the cvTerm to setpublic CvTerm getPsiModCvTerm()
public void setPsiModCvTerm(CvTerm cvTerm)
cvTerm
- the cvTerm to setpublic ModificationCategory getCategory()
public void setCategory(ModificationCategory category)
category
- the modification categoryCopyright © 2021. All rights reserved.