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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Ion
com.compomics.util.experiment.biology.ions.PrecursorIon
public class PrecursorIon
A precursor ion.
Nested Class Summary |
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Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.Ion |
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Ion.IonType |
Field Summary | |
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static int |
PRECURSOR
For now only one type of precursor implemented. |
Fields inherited from class com.compomics.util.experiment.biology.Ion |
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theoreticMass, type |
Constructor Summary | |
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PrecursorIon()
Constructor for a generic ion without neutral losses. |
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PrecursorIon(ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion. |
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PrecursorIon(double theoreticMass,
ArrayList<NeutralLoss> neutralLosses)
Constructor. |
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PrecursorIon(Peptide peptide)
Constructor. |
Method Summary | |
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String |
getName()
Returns the name of the ion. |
ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the possible neutral losses of this ion type. |
static ArrayList<Integer> |
getPossibleSubtypes()
Returns an arraylist of possible subtypes. |
CvTerm |
getPrideCvTerm()
Returns the pride 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.Ion |
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getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, setTheoreticMass |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int PRECURSOR
Constructor Detail |
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public PrecursorIon(double theoreticMass, ArrayList<NeutralLoss> neutralLosses)
theoreticMass
- the theoretic massneutralLosses
- the neutral lossespublic PrecursorIon(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- the neutral lossespublic PrecursorIon()
public PrecursorIon(Peptide peptide)
peptide
- the theoretic peptideMethod Detail |
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public String getName()
Ion
getName
in class Ion
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
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 ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
public boolean isSameAs(Ion anotherIon)
Ion
isSameAs
in class Ion
anotherIon
- the other ion
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