AnnotationSettings (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings

All Implemented Interfaces:

Serializable
```
public class AnnotationSettings
extends Object
implements Serializable
```
This class contains the spectrum annotation preferences.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

AnnotationSettings()
Constructor.

AnnotationSettings(SearchParameters searchParameters)
Constructor setting preferences from search parameters.

Constructors
Constructor and Description
`AnnotationSettings()` Constructor.
`AnnotationSettings(SearchParameters searchParameters)` Constructor setting preferences from search parameters.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addIonType(Ion.IonType ionType)` Adds a new ion type to annotate.
`void`	`addIonType(Ion.IonType ionType, int subType)` Adds a new ion type and subtype to annotate.
`void`	`addNeutralLoss(NeutralLoss neutralLoss)` Adds a neutral loss.
`Boolean`	`areNeutralLossesSequenceAuto()` Returns whether neutral losses are considered only for amino acids of interest or not.
`void`	`clearIonTypes()` Clears the ion types annotated.
`void`	`clearNeutralLosses()` Clears the considered neutral losses.
`AnnotationSettings`	`clone()` Clones the settings.
`double`	`getAnnotationIntensityLimit()` Returns the intensity percentile to consider for annotation.
`int`	`getDeNovoCharge()` Returns the charge to use for the fragment ions in the de novo sequencing.
`double`	`getFragmentIonAccuracy()` Returns the fragment ion accuracy.
`double`	`getFragmentIonAccuracyInDa(Double refMass)` Returns the fragment ion accuracy in Da.
`HashSet<Integer>`	`getFragmentIonTypes()` Returns the type of peptide fragment ions annotated.
`HashMap<Ion.IonType,HashSet<Integer>>`	`getIonTypes()` Returns the type of ions annotated.
`ArrayList<NeutralLoss>`	`getNeutralLosses()` Returns the considered neutral losses.
`Boolean`	`getRelatedIons()` Indicates whether related ions should be annotated by default.
`Boolean`	`getReporterIons()` Indicates whether reporter ions should be annotated by default.
`String`	`getShortDescription()` Returns a short description of the parameters.
`SpecificAnnotationSettings`	`getSpecificAnnotationPreferences(String spectrumKey, SpectrumIdentificationAssumption spectrumIdentificationAssumption, SequenceMatchingPreferences sequenceMatchingPreferences, SequenceMatchingPreferences ptmSequenceMatchingPreferences)` Returns the annotation preferences specific to a spectrum and an identification assumption.
`boolean`	`isAutomaticAnnotation()` Returns whether the annotation settings should be automatically inferred.
`boolean`	`isFragmentIonPpm()` Indicates whether the fragment ion accuracy is in ppm.
`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.
`boolean`	`isSameAs(AnnotationSettings annotationSettings)` Returns a boolean indicating whether the given annotation settings are the same as these ones.
`void`	`setAutomaticAnnotation(boolean automaticAnnotation)` Sets whether the annotation settings should be automatically inferred.
`void`	`setDeNovoCharge(int deNovoCharge)` Set the charge to use for the fragment ions in the de novo sequencing
`void`	`setFragmentIonAccuracy(double fragmentIonAccuracy)` Sets the fragment ion accuracy.
`void`	`setFragmentIonPpm(boolean fragmentIonPpm)` Sets whether the fragment ion accuracy is in ppm.
`void`	`setHighResolutionAnnotation(boolean highResolutionAnnotation)` Set if the peak annotation should be based on the most accurate mz value, or on the most intense peak.
`void`	`setIntensityLimit(double intensityLimit)` Sets the intensity percentile to consider for annotation.
`void`	`setNeutralLossesSequenceAuto(Boolean neutralLossesAuto)` Sets whether neutral losses are considered only for amino acids of interest or not.
`void`	`setPreferencesFromSearchParameters(SearchParameters searchParameters)` Updates the annotation parameters based on search parameters.
`void`	`setRelatedIons(Boolean relatedIons)` Sets whether related ions should be annotated by default.
`void`	`setReporterIons(Boolean reporterIons)` Sets whether reporter ions should be annotated by default.
`void`	`setShowAllPeaks(boolean showAllPeaks)` Set if all peaks or just the annotated ones are to be shown.
`void`	`setShowForwardIonDeNovoTags(boolean showForwardIonDeNovoTags)` Set if the automatic forward ion de novo tags are to be shown.
`void`	`setShowRewindIonDeNovoTags(boolean showRewindIonDeNovoTags)` Set if the automatic rewind ion de novo tags are to be shown.
`void`	`setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)` Set if the automatic y-axis zoom only considers the annotated peaks.
`boolean`	`showAllPeaks()` If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.
`boolean`	`showForwardIonDeNovoTags()` Returns true if the automatic forward ion de novo tags are to be shown.
`boolean`	`showRewindIonDeNovoTags()` Returns true if the automatic rewind ion de novo tags are to be shown.
`boolean`	`yAxisZoomExcludesBackgroundPeaks()` Returns true if the automatic y-axis zoom excludes background peaks.

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AnnotationSettings
```
public AnnotationSettings()
```
    Constructor.
  - AnnotationSettings
```
public AnnotationSettings(SearchParameters searchParameters)
```
    Constructor setting preferences from search parameters.
    
    Parameters:
    
    searchParameters - the search parameters
- Method Detail
  - getSpecificAnnotationPreferences
```
public SpecificAnnotationSettings getSpecificAnnotationPreferences(String spectrumKey,
                                                                   SpectrumIdentificationAssumption spectrumIdentificationAssumption,
                                                                   SequenceMatchingPreferences sequenceMatchingPreferences,
                                                                   SequenceMatchingPreferences ptmSequenceMatchingPreferences)
                                                            throws IOException,
                                                                   InterruptedException,
                                                                   ClassNotFoundException,
                                                                   SQLException
```
    Returns the annotation preferences specific to a spectrum and an identification assumption.
    
    Parameters:
    
    spectrumKey - the key of the spectrum to annotate
    
    spectrumIdentificationAssumption - the spectrum identification assumption to annotate with
    
    sequenceMatchingPreferences - the sequence matching preferences for peptide to protein mapping
    
    ptmSequenceMatchingPreferences - the sequence matching preferences for PTM to peptide mapping
    
    Returns:
    
    the annotation preferences specific to a spectrum and an identification assumption
    
    Throws:
    
    IOException - exception thrown whenever an error occurred while interacting with a file while mapping potential modification sites
    
    InterruptedException - exception thrown whenever a threading issue occurred while mapping potential modification sites
    
    ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object from the ProteinTree
    
    SQLException - exception thrown whenever an error occurred while interacting with the ProteinTree
  - setPreferencesFromSearchParameters
```
public void setPreferencesFromSearchParameters(SearchParameters searchParameters)
```
    Updates the annotation parameters based on search parameters.
    
    Parameters:
    
    searchParameters - the search parameters where to take the information from
  - areNeutralLossesSequenceAuto
```
public Boolean areNeutralLossesSequenceAuto()
```
    Returns whether neutral losses are considered only for amino acids of interest or not.
    
    Returns:
    
    a boolean indicating whether neutral losses are considered only for amino acids of interest or not
  - setNeutralLossesSequenceAuto
```
public void setNeutralLossesSequenceAuto(Boolean neutralLossesAuto)
```
    Sets whether neutral losses are considered only for amino acids of interest or not.
    
    Parameters:
    
    neutralLossesAuto - a boolean indicating whether neutral losses are considered only for amino acids of interest or not
  - getReporterIons
```
public Boolean getReporterIons()
```
    Indicates whether reporter ions should be annotated by default.
    
    Returns:
    
    a boolean indicating whether reporter ions should be annotated by default
  - setReporterIons
```
public void setReporterIons(Boolean reporterIons)
```
    Sets whether reporter ions should be annotated by default.
    
    Parameters:
    
    reporterIons - a boolean indicating whether reporter ions should be annotated by default
  - getRelatedIons
```
public Boolean getRelatedIons()
```
    Indicates whether related ions should be annotated by default.
    
    Returns:
    
    a boolean indicating whether related ions should be annotated by default
  - setRelatedIons
```
public void setRelatedIons(Boolean relatedIons)
```
    Sets whether related ions should be annotated by default.
    
    Parameters:
    
    relatedIons - a boolean indicating whether related ions should be annotated by default
  - clearNeutralLosses
```
public void clearNeutralLosses()
```
    Clears the considered neutral losses.
  - getNeutralLosses
```
public ArrayList<NeutralLoss> getNeutralLosses()
```
    Returns the considered neutral losses.
    
    Returns:
    
    the considered neutral losses
  - addNeutralLoss
```
public void addNeutralLoss(NeutralLoss neutralLoss)
```
    Adds a neutral loss.
    
    Parameters:
    
    neutralLoss - a new neutral loss
  - getIonTypes
```
public HashMap<Ion.IonType,HashSet<Integer>> getIonTypes()
```
    Returns the type of ions annotated.
    
    Returns:
    
    the type of ions annotated
  - getFragmentIonTypes
```
public HashSet<Integer> getFragmentIonTypes()
```
    Returns the type of peptide fragment ions annotated.
    
    Returns:
    
    the type of peptide fragment ions annotated
  - addIonType
```
public void addIonType(Ion.IonType ionType,
                       int subType)
```
    Adds a new ion type and subtype to annotate.
    
    Parameters:
    
    ionType - a new ion type to annotate
    
    subType - the ion sub type
  - addIonType
```
public void addIonType(Ion.IonType ionType)
```
    Adds a new ion type to annotate. All subtypes will be annotated.
    
    Parameters:
    
    ionType - a new ion type to annotate
  - clearIonTypes
```
public void clearIonTypes()
```
    Clears the ion types annotated.
  - setAutomaticAnnotation
```
public void setAutomaticAnnotation(boolean automaticAnnotation)
```
    Sets whether the annotation settings should be automatically inferred.
    
    Parameters:
    
    automaticAnnotation - a boolean indicating whether the annotation settings should be automatically inferred
  - isAutomaticAnnotation
```
public boolean isAutomaticAnnotation()
```
    Returns whether the annotation settings should be automatically inferred.
    
    Returns:
    
    a boolean indicating whether the annotation settings should be automatically inferred
  - getFragmentIonAccuracy
```
public double getFragmentIonAccuracy()
```
    Returns the fragment ion accuracy.
    
    Returns:
    
    the fragment ion accuracy
  - getFragmentIonAccuracyInDa
```
public double getFragmentIonAccuracyInDa(Double refMass)
```
    Returns the fragment ion accuracy in Da. If the tolerance is in ppm it will be converted using the given reference mass.
    
    Parameters:
    
    refMass - the reference mass to use for the ppm to Da conversion
    
    Returns:
    
    the fragment ion accuracy
  - setFragmentIonAccuracy
```
public void setFragmentIonAccuracy(double fragmentIonAccuracy)
```
    Sets the fragment ion accuracy.
    
    Parameters:
    
    fragmentIonAccuracy - the fragment ion accuracy
  - isFragmentIonPpm
```
public boolean isFragmentIonPpm()
```
    Indicates whether the fragment ion accuracy is in ppm.
    
    Returns:
    
    a boolean indicating whether the fragment ion accuracy is in ppm
  - setFragmentIonPpm
```
public void setFragmentIonPpm(boolean fragmentIonPpm)
```
    Sets whether the fragment ion accuracy is in ppm.
    
    Parameters:
    
    fragmentIonPpm - a boolean indicating whether the fragment ion accuracy is in ppm
  - getAnnotationIntensityLimit
```
public double getAnnotationIntensityLimit()
```
    Returns the intensity percentile to consider for annotation. e.g. 0.75 means that the 25% most intense peaks will be annotated.
    
    Returns:
    
    the intensityLimit
  - setIntensityLimit
```
public void setIntensityLimit(double intensityLimit)
```
    Sets the intensity percentile to consider for annotation. e.g. 0.75 means that the 25% most intense peaks will be annotated.
    
    Parameters:
    
    intensityLimit - the intensityLimit to set
  - showAllPeaks
```
public boolean showAllPeaks()
```
    If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.
    
    Returns:
    
    true if all peaks are to be shown
  - setShowAllPeaks
```
public void setShowAllPeaks(boolean showAllPeaks)
```
    Set if all peaks or just the annotated ones are to be shown.
    
    Parameters:
    
    showAllPeaks - if all peaks are to be shown
  - yAxisZoomExcludesBackgroundPeaks
```
public boolean yAxisZoomExcludesBackgroundPeaks()
```
    Returns true if the automatic y-axis zoom excludes background peaks. False if includes all peaks.
    
    Returns:
    
    true if the automatic y-axis zoom excludes background peaks
  - setYAxisZoomExcludesBackgroundPeaks
```
public void setYAxisZoomExcludesBackgroundPeaks(boolean yAxisZoomExcludesBackgroundPeaks)
```
    Set if the automatic y-axis zoom only considers the annotated peaks.
    
    Parameters:
    
    yAxisZoomExcludesBackgroundPeaks - if the automatic y-axis zoom only considers the annotated peaks
  - showForwardIonDeNovoTags
```
public boolean showForwardIonDeNovoTags()
```
    Returns true if the automatic forward ion de novo tags are to be shown.
    
    Returns:
    
    the showForwardIonDeNovoTags
  - setShowForwardIonDeNovoTags
```
public void setShowForwardIonDeNovoTags(boolean showForwardIonDeNovoTags)
```
    Set if the automatic forward ion de novo tags are to be shown.
    
    Parameters:
    
    showForwardIonDeNovoTags - the showForwardIonDeNovoTags to set
  - showRewindIonDeNovoTags
```
public boolean showRewindIonDeNovoTags()
```
    Returns true if the automatic rewind ion de novo tags are to be shown.
    
    Returns:
    
    the showRewindIonDeNovoTags
  - setShowRewindIonDeNovoTags
```
public void setShowRewindIonDeNovoTags(boolean showRewindIonDeNovoTags)
```
    Set if the automatic rewind ion de novo tags are to be shown.
    
    Parameters:
    
    showRewindIonDeNovoTags - the showRewindIonDeNovoTags to set
  - getDeNovoCharge
```
public int getDeNovoCharge()
```
    Returns the charge to use for the fragment ions in the de novo sequencing.
    
    Returns:
    
    the charge to use for the fragment ions in the de novo sequencing
  - setDeNovoCharge
```
public void setDeNovoCharge(int deNovoCharge)
```
    Set the charge to use for the fragment ions in the de novo sequencing
    
    Parameters:
    
    deNovoCharge - the charge to use for the fragment ions in the de novo sequencing
  - isHighResolutionAnnotation
```
public 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.
    
    Returns:
    
    the highResolutionAnnotation
  - setHighResolutionAnnotation
```
public void setHighResolutionAnnotation(boolean highResolutionAnnotation)
```
    Set if the peak annotation should be based on the most accurate mz value, or on the most intense peak.
    
    Parameters:
    
    highResolutionAnnotation - the highResolutionAnnotation to set
  - clone
```
public AnnotationSettings clone()
```
    Clones the settings.
    
    Overrides:
    
    clone in class Object
    
    Returns:
    
    a clone of this object
  - isSameAs
```
public boolean isSameAs(AnnotationSettings annotationSettings)
```
    Returns a boolean indicating whether the given annotation settings are the same as these ones.
    
    Parameters:
    
    annotationSettings - the annotation settings to compare to
    
    Returns:
    
    a boolean indicating whether the given annotation settings are the same as these ones
  - getShortDescription
```
public String getShortDescription()
```
    Returns a short description of the parameters.
    
    Returns:
    
    a short description of the parameters

Class AnnotationSettings

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AnnotationSettings

AnnotationSettings

Method Detail

getSpecificAnnotationPreferences

setPreferencesFromSearchParameters

areNeutralLossesSequenceAuto

setNeutralLossesSequenceAuto

getReporterIons

setReporterIons

getRelatedIons

setRelatedIons

clearNeutralLosses

getNeutralLosses

addNeutralLoss

getIonTypes

getFragmentIonTypes

addIonType

addIonType

clearIonTypes

setAutomaticAnnotation

isAutomaticAnnotation

getFragmentIonAccuracy

getFragmentIonAccuracyInDa

setFragmentIonAccuracy

isFragmentIonPpm

setFragmentIonPpm

getAnnotationIntensityLimit

setIntensityLimit

showAllPeaks

setShowAllPeaks

yAxisZoomExcludesBackgroundPeaks

setYAxisZoomExcludesBackgroundPeaks

showForwardIonDeNovoTags

setShowForwardIonDeNovoTags

showRewindIonDeNovoTags

setShowRewindIonDeNovoTags

getDeNovoCharge

setDeNovoCharge

isHighResolutionAnnotation

setHighResolutionAnnotation

clone

isSameAs

getShortDescription