Class PrecursorIon
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.Ion
com.compomics.util.experiment.biology.ions.impl.PrecursorIon
- All Implemented Interfaces:
Serializable
public class PrecursorIon extends Ion
A precursor ion.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Nested Class Summary
Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.ions.Ion
Ion.IonType
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Field Summary
Fields Modifier and Type Field Description static int
PRECURSOR
For now only one type of precursor implemented.Fields inherited from class com.compomics.util.experiment.biology.ions.Ion
atomChain, theoreticMass, theoreticMass1, type
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Constructor Summary
Constructors Constructor Description PrecursorIon()
Constructor for a generic ion without neutral losses.PrecursorIon(double theoreticMass)
Constructor for a generic ion without neutral losses.PrecursorIon(double theoreticMass, NeutralLoss[] neutralLosses)
Constructor.PrecursorIon(NeutralLoss[] neutralLosses)
Constructor for a generic ion. -
Method Summary
Modifier and Type Method Description String
getName()
Returns the name of the ion.NeutralLoss[]
getNeutralLosses()
Returns the possible neutral losses of this ion type.static int[]
getPossibleSubtypes()
Returns the possible subtypes.CvTerm
getPrideCvTerm()
Returns the CV term adapted to the fragment ion.CvTerm
getPsiMsCvTerm()
Returns the CV term adapted to the fragment ion.int
getSubType()
Returns the ion subtype.String
getSubTypeAsString()
Returns the subtype as string.boolean
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.Methods inherited from class com.compomics.util.experiment.biology.ions.Ion
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getPossibleSubtypesAsSet, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Field Details
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PRECURSOR
public static final int PRECURSORFor now only one type of precursor implemented.- See Also:
- Constant Field Values
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Constructor Details
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PrecursorIon
Constructor.- Parameters:
theoreticMass
- the theoretic massneutralLosses
- the neutral losses
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PrecursorIon
Constructor for a generic ion.- Parameters:
neutralLosses
- the neutral losses
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PrecursorIon
public PrecursorIon()Constructor for a generic ion without neutral losses. -
PrecursorIon
public PrecursorIon(double theoreticMass)Constructor for a generic ion without neutral losses.- Parameters:
theoreticMass
- the theoretic mass of the precursor
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Method Details
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getName
Description copied from class:Ion
Returns the name of the ion. The name should be short enough to be displayed on a spectrum. -
getPrideCvTerm
Description copied from class:Ion
Returns the CV term adapted to the fragment ion. Null if none corresponding.- Specified by:
getPrideCvTerm
in classIon
- Returns:
- the CV term adapted to the fragment ion. Null if none corresponding
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getPsiMsCvTerm
Description copied from class:Ion
Returns the CV term adapted to the fragment ion. Null if none corresponding.- Specified by:
getPsiMsCvTerm
in classIon
- Returns:
- the CV term adapted to the fragment ion. Null if none corresponding
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getSubType
public int getSubType()Description copied from class:Ion
Returns the ion subtype.- Specified by:
getSubType
in classIon
- Returns:
- the ion subtype as integer
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getSubTypeAsString
Description copied from class:Ion
Returns the subtype as string.- Specified by:
getSubTypeAsString
in classIon
- Returns:
- the subtype as string
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getPossibleSubtypes
public static int[] getPossibleSubtypes()Returns the possible subtypes.- Returns:
- the possible subtypes
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getNeutralLosses
Description copied from class:Ion
Returns the possible neutral losses of this ion type. An empty list if none.- Specified by:
getNeutralLosses
in classIon
- Returns:
- the possible neutral losses of this ion type
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isSameAs
Description copied from class:Ion
Returns a boolean indicating whether the ion is the same as another ion.
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