public class ElementaryIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
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static ElementaryIon |
proton
A proton.
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static int |
PROTON
Subtype int for a proton.
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static double[] |
protonMassMultiples
Cache for the multiples of the proton mass.
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atomChain, theoreticMass, theoreticMass1, type
NO_KEY
Constructor and Description |
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ElementaryIon()
Empty default constructor
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ElementaryIon(String name,
double theoreticMass,
int subType)
Constructor.
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Modifier and Type | Method and Description |
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String |
getName()
Returns the name of the ion.
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NeutralLoss[] |
getNeutralLosses()
Returns the possible neutral losses of this ion type.
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static int[] |
getPossibleSubtypes()
Returns the possible subtypes.
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CvTerm |
getPrideCvTerm()
Returns the CV term adapted to the fragment ion.
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static double |
getProtonMassMultiple(int i)
Returns the mass of the proton multiplied by i.
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CvTerm |
getPsiMsCvTerm()
Returns the CV term adapted to the fragment ion.
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int |
getSubType()
Returns the ion subtype.
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String |
getSubTypeAsString()
Returns the subtype as string.
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boolean |
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
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getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getPossibleSubtypesAsSet, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final int PROTON
public static final ElementaryIon proton
public static double[] protonMassMultiples
public ElementaryIon()
public ElementaryIon(String name, double theoreticMass, int subType)
name
- the name of the iontheoreticMass
- the theoretic mass of the ionsubType
- the subtype indexpublic static double getProtonMassMultiple(int i)
i
- ipublic String getName()
Ion
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public CvTerm getPsiMsCvTerm()
Ion
getPsiMsCvTerm
in class Ion
public int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static int[] getPossibleSubtypes()
public NeutralLoss[] getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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