public class PrecursorIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
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static int |
PRECURSOR
For now only one type of precursor implemented.
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atomChain, theoreticMass, theoreticMass1, type
Constructor and Description |
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PrecursorIon()
Constructor for a generic ion without neutral losses.
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PrecursorIon(double theoreticMass)
Constructor for a generic ion without neutral losses.
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PrecursorIon(double theoreticMass,
NeutralLoss[] neutralLosses)
Constructor.
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PrecursorIon(NeutralLoss[] neutralLosses)
Constructor for a generic ion.
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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 ArrayList<Integer> |
getPossibleSubtypes()
Returns an arraylist of possible subtypes.
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CvTerm |
getPrideCvTerm()
Returns the CV term adapted to the fragment ion.
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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, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, clearParametersMap, getUrParam, removeUrParam
public static final int PRECURSOR
public PrecursorIon(double theoreticMass, NeutralLoss[] neutralLosses)
theoreticMass
- the theoretic massneutralLosses
- the neutral lossespublic PrecursorIon(NeutralLoss[] neutralLosses)
neutralLosses
- the neutral lossespublic PrecursorIon()
public PrecursorIon(double theoreticMass)
theoreticMass
- the theoretic mass of the precursorpublic 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 ArrayList<Integer> getPossibleSubtypes()
public NeutralLoss[] getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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