public class SpecificAnnotationSettings extends Object
Constructor and Description |
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SpecificAnnotationSettings(String spectrumKey,
SpectrumIdentificationAssumption spectrumIdentificationAssumption)
Constructor.
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Modifier and Type | Method and Description |
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void |
addIonType(Ion.IonType ionType)
Adds a new ion type to annotate.
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void |
addIonType(Ion.IonType ionType,
int subType)
Adds a new ion type and subtype to annotate.
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void |
addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
addSelectedCharge(int selectedCharge)
Add a charge to take into account when annotating the spectrum.
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void |
clearCharges()
Clears the selected charges.
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void |
clearIonTypes()
Clears the ion types annotated.
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void |
clearNeutralLosses()
Clears the considered neutral losses.
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SpecificAnnotationSettings |
clone() |
double |
getFragmentIonAccuracy()
Returns the fragment ion accuracy.
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double |
getFragmentIonAccuracyInDa(Double refMass)
Returns the fragment ion accuracy in Da.
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HashSet<Integer> |
getFragmentIonTypes()
Returns the type of peptide fragment ions annotated.
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HashMap<Ion.IonType,HashSet<Integer>> |
getIonTypes()
Returns the map of ions to annotate.
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NeutralLossesMap |
getNeutralLossesMap()
Returns the map of neutral losses to annotate.
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int |
getPrecursorCharge()
Returns the charge of the precursor.
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ArrayList<Integer> |
getSelectedCharges()
Returns the charges selected for annotation.
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SpectrumIdentificationAssumption |
getSpectrumIdentificationAssumption()
Returns the spectrum identification assumption to annotate with.
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String |
getSpectrumKey()
Returns the key of the spectrum to annotate.
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boolean |
isFragmentIonPpm()
Indicates whether the fragment ion accuracy is in ppm.
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boolean |
isNeutralLossesAuto()
Indicates whether neutral losses should be automatically selected.
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void |
setFragmentIonAccuracy(double fragmentIonAccuracy)
Sets the fragment ion accuracy.
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void |
setFragmentIonPpm(boolean fragmentIonPpm)
Sets whether the fragment ion accuracy is in ppm.
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void |
setNeutralLossesAuto(boolean neutralLossesAuto)
Sets whether neutral losses should be automatically selected.
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void |
setNeutralLossesMap(NeutralLossesMap neutralLossesMap)
Sets the map of neutral losses to annotate.
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void |
setSelectedCharges(ArrayList<Integer> selectedCharges)
Sets the charges selected for annotation.
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void |
setSelectedIonsMap(HashMap<Ion.IonType,HashSet<Integer>> selectedIonsMap)
Sets the map of ions to annotate.
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public SpecificAnnotationSettings(String spectrumKey, SpectrumIdentificationAssumption spectrumIdentificationAssumption)
spectrumKey
- the key of the spectrum to annotatespectrumIdentificationAssumption
- the spectrum identification
assumption to annotate withpublic String getSpectrumKey()
public SpectrumIdentificationAssumption getSpectrumIdentificationAssumption()
public int getPrecursorCharge()
public HashMap<Ion.IonType,HashSet<Integer>> getIonTypes()
public HashSet<Integer> getFragmentIonTypes()
public void setSelectedIonsMap(HashMap<Ion.IonType,HashSet<Integer>> selectedIonsMap)
selectedIonsMap
- the map of ions to annotatepublic void clearIonTypes()
public void addIonType(Ion.IonType ionType, int subType)
ionType
- a new ion type to annotatesubType
- the ion sub typepublic void addIonType(Ion.IonType ionType)
ionType
- a new ion type to annotatepublic NeutralLossesMap getNeutralLossesMap()
public void setNeutralLossesMap(NeutralLossesMap neutralLossesMap)
neutralLossesMap
- the map of neutral losses to annotatepublic void clearNeutralLosses()
public void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- a new neutral losspublic ArrayList<Integer> getSelectedCharges()
public void setSelectedCharges(ArrayList<Integer> selectedCharges)
selectedCharges
- the charges selected for annotationpublic void clearCharges()
public void addSelectedCharge(int selectedCharge)
selectedCharge
- a charge to take into account when annotating the
spectrumpublic double getFragmentIonAccuracy()
public double getFragmentIonAccuracyInDa(Double refMass)
refMass
- the reference mass to use for the ppm to Da conversionpublic void setFragmentIonAccuracy(double fragmentIonAccuracy)
fragmentIonAccuracy
- the fragment ion accuracypublic boolean isFragmentIonPpm()
public void setFragmentIonPpm(boolean fragmentIonPpm)
fragmentIonPpm
- a boolean indicating whether the fragment ion
accuracy is in ppmpublic boolean isNeutralLossesAuto()
public void setNeutralLossesAuto(boolean neutralLossesAuto)
neutralLossesAuto
- a boolean indicating whether neutral losses
should be automatically selectedpublic SpecificAnnotationSettings clone()
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