public class AnnotationPreferences extends Object implements Serializable
Constructor and Description |
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AnnotationPreferences()
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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boolean |
areNeutralLossesSequenceDependant()
Returns whether neutral losses are considered only for amino acids of
interest or not.
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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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double |
getAnnotationIntensityLimit()
Returns the intensity limit.
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int |
getCurrentPrecursorCharge()
Returns the current precursor charge.
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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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ArrayList<Integer> |
getFragmentIonTypes()
Returns the type of peptide fragment ions annotated.
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HashMap<Ion.IonType,ArrayList<Integer>> |
getIonTypes()
Returns the type of ions annotated.
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NeutralLossesMap |
getNeutralLosses()
Returns the considered neutral losses.
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ArrayList<Integer> |
getValidatedCharges()
Returns the fragment ion charges considered for the desired precursor
charge.
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boolean |
isHighResolutionAnnotation()
Returns true if the peak annotation should be based on the most accurate
mz value, false bases the annotation on the most intense peak.
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void |
resetAutomaticAnnotation(AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Updates the neutral losses and charge annotation settings.
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void |
setAnnotationLevel(double intensityLimit)
Sets the annotation level.
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void |
setCurrentSettings(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
boolean newSpectrum,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Sets the annotation settings for the current peptide and precursor
charge.
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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 |
setHighResolutionAnnotation(boolean highResolutionAnnotation)
Set if the peak annotation should be based on the most accurate
mz value, or on the most intense peak.
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void |
setIntensityIonTable(boolean intensityIonTable)
Set if the intensity or m/z ion table should be shown.
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void |
setNeutralLossesSequenceDependant(boolean neutralLossesSequenceDependant)
Set whether neutral losses are considered only for amino acids of
interest or not.
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void |
setPreferencesFromSearchParameters(SearchParameters searchParameters)
Updates the annotation parameters based on the search parameters
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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 |
setShowBars(boolean showBars)
Set if the bars in the bubble plot are to be shown or not.
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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 |
setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)
Set if the automatic y-axis zoom only considers the anotated 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 |
showBars()
If true, bars are shown in the bubble plot highlighting the ions.
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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 |
useAutomaticAnnotation()
Returns whether PeptideShaker should automatically set the annotations.
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void |
useAutomaticAnnotation(boolean automaticAnnotation)
Sets whether the default PeptideShaker annotation should be used.
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boolean |
useIntensityIonTable()
If true, the ion table is shown as an intensity versionm, false displays
the standard Mascot version.
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boolean |
yAxisZoomExcludesBackgroundPeaks()
Returns true if the automatic y-axis zoom excludes background peaks.
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public void setPreferencesFromSearchParameters(SearchParameters searchParameters)
searchParameters
- the search parameters where to take the
information frompublic void setCurrentSettings(SpectrumIdentificationAssumption spectrumIdentificationAssumption, boolean newSpectrum, AminoAcidPattern.MatchingType matchingType, double mzTolerance) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
spectrumIdentificationAssumption
- the spectrum identification
assumptionnewSpectrum
- boolean indicating whether this is a new spectrummatchingType
- the matching type to map ptms on the peptide sequencemzTolerance
- the ms2 m/z tolerance to useIOException
- exception thrown whenever an error occurred while
reading a protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequenceFileNotFoundException
ClassNotFoundException
SQLException
public void resetAutomaticAnnotation(AminoAcidPattern.MatchingType matchingType, double mzTolerance) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException, SQLException
matchingType
- the matching type to map ptms on the peptide sequencemzTolerance
- the ms2 m/z tolerance to useIOException
- exception thrown whenever an error occurred while
reading a protein sequenceIllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequenceInterruptedException
- exception thrown whenever an error occurred
while reading a protein sequenceFileNotFoundException
ClassNotFoundException
SQLException
public boolean areNeutralLossesSequenceDependant()
public void setNeutralLossesSequenceDependant(boolean neutralLossesSequenceDependant)
neutralLossesSequenceDependant
- public ArrayList<Integer> getValidatedCharges()
public void clearCharges()
public void addSelectedCharge(int selectedCharge)
selectedCharge
- a charge to take into account when annotating the
spectrumpublic void clearNeutralLosses()
public NeutralLossesMap getNeutralLosses()
public void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- a new neutral losspublic HashMap<Ion.IonType,ArrayList<Integer>> getIonTypes()
public ArrayList<Integer> getFragmentIonTypes()
public 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 void useAutomaticAnnotation(boolean automaticAnnotation)
automaticAnnotation
- a boolean indicating whether the default
PeptideShaker annotation should be usedpublic boolean useAutomaticAnnotation()
public double getFragmentIonAccuracy()
public void setFragmentIonAccuracy(double fragmentIonAccuracy)
fragmentIonAccuracy
- the fragment ion accuracypublic int getCurrentPrecursorCharge()
public double getAnnotationIntensityLimit()
public void setAnnotationLevel(double intensityLimit)
intensityLimit
- the intensityLimit to setpublic boolean showAllPeaks()
public void setShowAllPeaks(boolean showAllPeaks)
showAllPeaks
- public boolean showBars()
public void setShowBars(boolean showBars)
showBars
- public boolean useIntensityIonTable()
public void setIntensityIonTable(boolean intensityIonTable)
intensityIonTable
- public boolean yAxisZoomExcludesBackgroundPeaks()
public void setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)
yAxisZoomExcludesBackgroundPeaks
- public 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 boolean isHighResolutionAnnotation()
public void setHighResolutionAnnotation(boolean highResolutionAnnotation)
highResolutionAnnotation
- the highResolutionAnnotation to setCopyright © 2014. All rights reserved.