public class AnnotationParameters extends ExperimentObject
Modifier and Type | Class and Description |
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static class |
AnnotationParameters.IntensityThresholdType
Enum of the types of intensity thresholds available.
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NO_KEY
Constructor and Description |
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AnnotationParameters()
Constructor.
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AnnotationParameters(SearchParameters searchParameters)
Constructor setting preferences from search parameters.
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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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boolean |
areNeutralLossesSequenceAuto()
Returns whether neutral losses are considered only for amino acids of
interest or not.
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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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AnnotationParameters |
clone()
Clones the settings.
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double |
getAnnotationIntensityLimit()
Returns the intensity percentile to consider for annotation.
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int |
getDeNovoCharge()
Returns the charge to use for the fragment ions in the de novo
sequencing.
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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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AnnotationParameters.IntensityThresholdType |
getIntensityThresholdType()
Returns the intensity threshold type.
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HashMap<Ion.IonType,HashSet<Integer>> |
getIonTypes()
Returns the type of ions annotated.
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ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the considered neutral losses.
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boolean |
getRelatedIons()
Indicates whether related ions should be annotated by default.
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boolean |
getReporterIons()
Indicates whether reporter ions should be annotated by default.
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String |
getShortDescription()
Returns a short description of the parameters.
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SpecificAnnotationParameters |
getSpecificAnnotationParameters(String spectrumFile,
String spectrumTitle,
SpectrumIdentificationAssumption spectrumIdentificationAssumption,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
SpectrumAnnotator spectrumAnnotator)
Returns the annotation preferences specific to a spectrum and an
identification assumption.
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SpectrumAnnotator.TiesResolution |
getTiesResolution()
Returns the ties resolution method to use when multiple peaks can be
assigned to an ion.
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boolean |
isAutomaticAnnotation()
Returns whether the annotation settings should be automatically inferred.
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boolean |
isFragmentIonPpm()
Indicates whether the fragment ion accuracy is in ppm.
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boolean |
isSameAs(AnnotationParameters annotationSettings)
Returns a boolean indicating whether the given annotation settings are
the same as these ones.
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void |
setAutomaticAnnotation(boolean automaticAnnotation)
Sets whether the annotation settings should be automatically inferred.
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void |
setDeNovoCharge(int deNovoCharge)
Set the charge to use for the fragment ions in the de novo sequencing
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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 |
setIntensityLimit(double intensityLimit)
Sets the intensity percentile to consider for annotation.
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void |
setIntensityThresholdType(AnnotationParameters.IntensityThresholdType intensityThresholdType)
Sets the intensity threshold type.
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void |
setNeutralLossesSequenceAuto(boolean neutralLossesAuto)
Sets whether neutral losses are considered only for amino acids of
interest or not.
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void |
setParametersFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on search parameters.
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void |
setRelatedIons(boolean relatedIons)
Sets whether related ions should be annotated by default.
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void |
setReporterIons(boolean reporterIons)
Sets whether reporter ions should be annotated by default.
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void |
setShowAllPeaks(boolean showAllPeaks)
Set if all peaks or just the annotated ones are to be shown.
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void |
setShowForwardIonDeNovoTags(boolean showForwardIonDeNovoTags)
Set if the automatic forward ion de novo tags are to be shown.
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void |
setShowRewindIonDeNovoTags(boolean showRewindIonDeNovoTags)
Set if the automatic rewind ion de novo tags are to be shown.
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void |
setTiesResolution(SpectrumAnnotator.TiesResolution tiesResolution)
Sets the ties resolution method to use when multiple peaks can be
assigned to an ion.
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void |
setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)
Set if the automatic y-axis zoom only considers the annotated peaks.
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boolean |
showAllPeaks()
If true, all peaks are shown, false displays the annotated peaks, and the
non-annotated in the background.
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boolean |
showForwardIonDeNovoTags()
Returns true if the automatic forward ion de novo tags are to be shown.
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boolean |
showRewindIonDeNovoTags()
Returns true if the automatic rewind ion de novo tags are to be shown.
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boolean |
yAxisZoomExcludesBackgroundPeaks()
Returns true if the automatic y-axis zoom excludes background peaks.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public AnnotationParameters()
public AnnotationParameters(SearchParameters searchParameters)
searchParameters
- the search parameterspublic SpecificAnnotationParameters getSpecificAnnotationParameters(String spectrumFile, String spectrumTitle, SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, SpectrumAnnotator spectrumAnnotator)
spectrumFile
- the file of the spectrum to annotatespectrumTitle
- the title of the spectrum to annotatespectrumIdentificationAssumption
- the spectrum identification
assumption to annotate withmodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching
preferences for modification to peptide mappingspectrumAnnotator
- the spectrum annotatorpublic void setParametersFromSearchParameters(SearchParameters searchParameters)
searchParameters
- the search parameters where to take the
information frompublic boolean areNeutralLossesSequenceAuto()
public void setNeutralLossesSequenceAuto(boolean neutralLossesAuto)
neutralLossesAuto
- a boolean indicating whether neutral losses are
considered only for amino acids of interest or notpublic boolean getReporterIons()
public void setReporterIons(boolean reporterIons)
reporterIons
- a boolean indicating whether reporter ions should be
annotated by defaultpublic boolean getRelatedIons()
public void setRelatedIons(boolean relatedIons)
relatedIons
- a boolean indicating whether related ions should be
annotated by defaultpublic void clearNeutralLosses()
public ArrayList<NeutralLoss> getNeutralLosses()
public void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- a new neutral losspublic HashMap<Ion.IonType,HashSet<Integer>> getIonTypes()
public HashSet<Integer> getFragmentIonTypes()
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 void clearIonTypes()
public void setAutomaticAnnotation(boolean automaticAnnotation)
automaticAnnotation
- a boolean indicating whether the annotation
settings should be automatically inferredpublic boolean isAutomaticAnnotation()
public 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 double getAnnotationIntensityLimit()
public void setIntensityLimit(double intensityLimit)
intensityLimit
- the intensityLimit to setpublic AnnotationParameters.IntensityThresholdType getIntensityThresholdType()
public void setIntensityThresholdType(AnnotationParameters.IntensityThresholdType intensityThresholdType)
intensityThresholdType
- the intensity threshold typepublic boolean showAllPeaks()
public void setShowAllPeaks(boolean showAllPeaks)
showAllPeaks
- if all peaks are to be shownpublic boolean yAxisZoomExcludesBackgroundPeaks()
public void setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)
yAxisZoomExcludesBackgroundPeaks
- if the automatic y-axis zoom only
considers the annotated peakspublic boolean showForwardIonDeNovoTags()
public void setShowForwardIonDeNovoTags(boolean showForwardIonDeNovoTags)
showForwardIonDeNovoTags
- the showForwardIonDeNovoTags to setpublic boolean showRewindIonDeNovoTags()
public void setShowRewindIonDeNovoTags(boolean showRewindIonDeNovoTags)
showRewindIonDeNovoTags
- the showRewindIonDeNovoTags to setpublic int getDeNovoCharge()
public void setDeNovoCharge(int deNovoCharge)
deNovoCharge
- the charge to use for the fragment ions in the de
novo sequencingpublic SpectrumAnnotator.TiesResolution getTiesResolution()
public void setTiesResolution(SpectrumAnnotator.TiesResolution tiesResolution)
tiesResolution
- the ties resolution method to usepublic AnnotationParameters clone()
public boolean isSameAs(AnnotationParameters annotationSettings)
annotationSettings
- the annotation settings to compare topublic String getShortDescription()
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