Class ImmoniumIon
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.ions.Ion
com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
- All Implemented Interfaces:
Serializable
public class ImmoniumIon extends Ion
Represents an immonium ion.
- Author:
- Marc Vaudel, Harald Barsnes
- 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 char
aa
The amino acid that can generate this ion as single letter code.static ImmoniumIon
ALANINE
Alanine immonium ion.static ImmoniumIon
ARGININE
Arginine immonium ion.static ImmoniumIon
ASPARAGINE
Asparagine immonium ion.static ImmoniumIon
ASPARTIC_ACID
Aspartic acid immonium ion.static ImmoniumIon
CYSTEINE
Cysteine immonium ion.static ImmoniumIon
GLUTAMIC_ACID
Glutamic acid immonium ion.static ImmoniumIon
GLUTAMINE
Glutamine immonium ion.static ImmoniumIon
GLYCINE
Glycine immonium ion.static ImmoniumIon
HISTIDINE
Histidine immonium ion.static ImmoniumIon
ISOLEUCINE
Isoleucine immonium ion.static ImmoniumIon
LEUCINE
Leucine immonium ion.static ImmoniumIon
LYSINE
Lysine immonium ion.static ImmoniumIon
METHIONINE
Methionine immonium ion.static ImmoniumIon
PHENYLALANINE
Phenylananine immonium ion.static ImmoniumIon
PROLINE
Proline immonium ion.static ImmoniumIon
PYRROLYSINE
Pyrrolysine immonium ion.static ImmoniumIon
SELENOCYSTEINE
Selenocysteine immonium ion.static ImmoniumIon
SERINE
Serine immonium ion.static ImmoniumIon
THREONINE
Threonine immonium ion.static ImmoniumIon
TRYPTOPHAN
Tryptophan immonium ion.static ImmoniumIon
TYROSINE
Tyrosine immonium ion.static ImmoniumIon
VALINE
Valine immonium ion.Fields inherited from class com.compomics.util.experiment.biology.ions.Ion
atomChain, theoreticMass, theoreticMass1, type
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Constructor Summary
Constructors Constructor Description ImmoniumIon()
Empty default constructor -
Method Summary
Modifier and Type Method Description static ImmoniumIon
getImmoniumIon(char residue)
Returns the immonium ion produced by the given amino acid.static ImmoniumIon
getImmoniumIon(int subType)
Returns the immonium ion corresponding to the given subtype.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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ALANINE
Alanine immonium ion. -
ARGININE
Arginine immonium ion. -
ASPARAGINE
Asparagine immonium ion. -
ASPARTIC_ACID
Aspartic acid immonium ion. -
CYSTEINE
Cysteine immonium ion. -
GLUTAMIC_ACID
Glutamic acid immonium ion. -
GLUTAMINE
Glutamine immonium ion. -
GLYCINE
Glycine immonium ion. -
HISTIDINE
Histidine immonium ion. -
ISOLEUCINE
Isoleucine immonium ion. -
LEUCINE
Leucine immonium ion. -
LYSINE
Lysine immonium ion. -
METHIONINE
Methionine immonium ion. -
PHENYLALANINE
Phenylananine immonium ion. -
PROLINE
Proline immonium ion. -
SELENOCYSTEINE
Selenocysteine immonium ion. -
SERINE
Serine immonium ion. -
THREONINE
Threonine immonium ion. -
TRYPTOPHAN
Tryptophan immonium ion. -
TYROSINE
Tyrosine immonium ion. -
VALINE
Valine immonium ion. -
PYRROLYSINE
Pyrrolysine immonium ion. -
aa
public final char aaThe amino acid that can generate this ion as single letter code.
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Constructor Details
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ImmoniumIon
public ImmoniumIon()Empty default constructor
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Method Details
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getImmoniumIon
Returns the immonium ion corresponding to the given subtype.- Parameters:
subType
- the subtype- Returns:
- the immonium ion
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getImmoniumIon
Returns the immonium ion produced by the given amino acid.- Parameters:
residue
- the amino acid as char- Returns:
- the immonium ion
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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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