Class SpectrumPanel

All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible

public class SpectrumPanel
extends GraphicsPanel
This class presents a JPanel that will hold and display a mass spectrum in centroid or profile mode.
Version:
$Id: SpectrumPanel.java,v 1.9 2009/08/17 15:15:28 lennart Exp $
Author:
Lennart Martens, Harald Barsnes, Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile as an interactive lines plot.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, boolean aEnableInteraction)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile as a line plot.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aDrawStyle - the drawing style to use.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, Color aSpectrumFilenameColor)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aDrawStyle - the drawing style to use.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
      aSpectrumFilenameColor - Color with the color for the spectrumfilename on the panel can be 'null' for default coloring.
    • SpectrumPanel

      public SpectrumPanel()
      Empty default constructor
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aDrawStyle - the drawing style to use.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
      aSpectrumFilenameColor - Color with the color for the spectrumfilename on the panel can be 'null' for default coloring.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aDrawStyle - the drawing style to use.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
      aSpectrumFilenameColor - Color with the color for the spectrum filename in the panel can be 'null' for default coloring.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
      aShowPrecursorDetails - boolean that specifies if the precursor details should be shown in the panel
      aShowResolution - boolean that specifies if the resolution should be shown in the panel
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aDrawStyle - the drawing style to use.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
      aSpectrumFilenameColor - Color with the color for the spectrum filename in the panel can be 'null' for default coloring.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
      aShowPrecursorDetails - boolean that specifies if the precursor details should be shown in the panel
      aShowResolution - boolean that specifies if the resolution should be shown in the panel
      aMSLevel - int with the ms level for the spectrum
    • SpectrumPanel

      public SpectrumPanel​(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel, boolean aProfileMode)
      This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile with the specified drawing style.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
      aDrawStyle - the drawing style to use.
      aEnableInteraction - boolean that specifies whether user-derived events should be caught and dealt with.
      aSpectrumFilenameColor - Color with the color for the spectrum filename in the panel can be 'null' for default coloring.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
      aShowPrecursorDetails - boolean that specifies if the precursor details should be shown in the panel
      aShowResolution - boolean that specifies if the resolution should be shown in the panel
      aMSLevel - int with the ms level for the spectrum, set to 0 if ms level is unknown
      aProfileMode - boolean if set to true the spectrum will be drawn in profile mode
    • SpectrumPanel

      public SpectrumPanel​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName)
      This constructor creates a SpectrumPanel based on the passed parameters. This constructor will be used to annotate matched ions on the spectrum panels.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values.
      aPrecursorMZ - double with the precursor mass.
      aPrecursorCharge - String with the precursor intensity.
      aFileName - String with the title of the Query.
    • SpectrumPanel

      public SpectrumPanel​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, boolean aShowFileName)
      This constructor creates a SpectrumPanel based on the passed parameters. This constructor will be used to annotate matched ions on the spectrum panels.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values.
      aPrecursorMZ - double with the precursor mass.
      aPrecursorCharge - String with the precursor intensity.
      aFileName - String with the title of the Query.
      aShowFileName - boolean that specifies if the file name should be shown in the panel.
    • SpectrumPanel

      public SpectrumPanel​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, int aMaxPadding, boolean aShowFileName)
      This constructor creates a SpectrumPanel based on the passed parameters. This constructor will be used to annotate matched ions on the spectrum panels.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values.
      aPrecursorMZ - double with the precursor mass.
      aPrecursorCharge - String with the precursor intensity.
      aFileName - String with the title of the Query.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel.
    • SpectrumPanel

      public SpectrumPanel​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution)
      This constructor creates a SpectrumPanel based on the passed parameters. This constructor will be used to annotate matched ions on the spectrum panels.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values.
      aPrecursorMZ - double with the precursor mass.
      aPrecursorCharge - String with the precursor intensity.
      aFileName - String with the title of the Query.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
      aShowPrecursorDetails - boolean that specifies if the precursor details should be shown in the panel
      aShowResolution - boolean that specifies if the resolution should be shown in the panel
    • SpectrumPanel

      public SpectrumPanel​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel)
      This constructor creates a SpectrumPanel based on the passed parameters. This constructor will be used to annotate matched ions on the spectrum panels.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values.
      aPrecursorMZ - double with the precursor mass.
      aPrecursorCharge - String with the precursor intensity.
      aFileName - String with the title of the Query.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
      aShowPrecursorDetails - boolean that specifies if the precursor details should be shown in the panel
      aShowResolution - boolean that specifies if the resolution should be shown in the panel
      aMSLevel - int with the ms level for the spectrum, set to 0 if ms level is unknown
    • SpectrumPanel

      public SpectrumPanel​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel, boolean aProfileMode)
      This constructor creates a SpectrumPanel based on the passed parameters. This constructor will be used to annotate matched ions on the spectrum panels.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values.
      aPrecursorMZ - double with the precursor mass.
      aPrecursorCharge - String with the precursor charge.
      aFileName - String with the title of the Query.
      aMaxPadding - int the sets the maximum padding size.
      aShowFileName - boolean that specifies if the file name should be shown in the panel
      aShowPrecursorDetails - boolean that specifies if the precursor details should be shown in the panel
      aShowResolution - boolean that specifies if the resolution should be shown in the panel
      aMSLevel - int with the ms level for the spectrum, set to 0 if ms level is unknown
      aProfileMode - boolean if set to true the spectrum will be drawn in profile mode
  • Method Details

    • addMirroredSpectrum

      public void addMirroredSpectrum​(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, boolean aProfileMode, Color aSpectrumPeakColor, Color aSpectrumProfileModeLineColor)
      Add a mirrored spectrum (or chromatogram).
      Parameters:
      aXAxisData - the x axis data
      aYAxisData - the y axis data
      aPrecursorMZ - the precursor m/z
      aPrecursorCharge - the precursor charge
      aFileName - the file name
      aProfileMode - if the spectrum is to be drawn in profile mode
      aSpectrumPeakColor - the spectrum peak color
      aSpectrumProfileModeLineColor - the spectrum profile mode line color
    • addAdditionalDataset

      public void addAdditionalDataset​(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)
      Adds an additional spectrum dataset to be displayed in the same Spectrum Panel. Remember to use different colors for the different datasets.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values
      dataPointAndLineColor - the color to use for the data points and lines
      areaUnderCurveColor - the color to use for the area under the curve
    • addAdditionalMirroredDataset

      public void addAdditionalMirroredDataset​(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)
      Adds an additional mirrored spectrum dataset to be displayed in the same Spectrum Panel. Remember to use different colors for the different datasets.
      Parameters:
      aXAxisData - double[] with all the x-axis values.
      aYAxisData - double[] with all the y-axis values
      dataPointAndLineColor - the color to use for the data points and lines
      areaUnderCurveColor - the color to use for the area under the curve
    • setProfileMode

      public void setProfileMode​(boolean aProfileMode)
      Change the drawing type of the spectrum. Profile or centroid mode.
      Parameters:
      aProfileMode - if true, the spectrum is drawn in profile mode
    • setSpectrumPeakColor

      public void setSpectrumPeakColor​(Color aSpectrumPeakColor)
      Set the default spectrum peak color. (Note that this only has an impact on the first spectrum added. For additional spectra or mirrored spectra set the color in the given constructor.)
      Parameters:
      aSpectrumPeakColor - the color to set
    • setSpectrumProfileModeLineColor

      public void setSpectrumProfileModeLineColor​(Color aSpectrumProfileModeLineColor)
      Set the default spectrum profile mode color. (Note that this only has an impact on the first spectrum added. For additional spectra or mirrored spectra set the color in the given constructor.)
      Parameters:
      aSpectrumProfileModeLineColor - the color to set
    • showAnnotatedPeaksOnly

      public void showAnnotatedPeaksOnly​(boolean aAnnotatedPeaks)
      If true only the annotated peaks will be drawn. The default value is false, and result in all peaks being drawn. Note that this setting is ignored when in profile mode!
      Parameters:
      aAnnotatedPeaks - if true only the annotated peaks will be drawn
    • setSpectrumFile

      public void setSpectrumFile​(SpectrumFile aSpecFile)
      This method initializes a SpectrumPanel based on the spectrum information in the specified SpectrumFile.
      Parameters:
      aSpecFile - SpectrumFile with the information about masses and intensities that will be copied here. Note that mass-sorting will take place in this step as well.
    • determineColorOfPeak

      public static Color determineColorOfPeak​(String peakLabel)
      Deprecated.
      it is advised to use methods based on the ion type rather than on the peak label
      Returns the peak color to be used for the given peak label. The colors used are based on the color coding used in MascotDatfile.
      Parameters:
      peakLabel - the peak label
      Returns:
      the peak color
    • filterAnnotations

      public static Vector<SpectrumAnnotation> filterAnnotations​(Vector<SpectrumAnnotation> annotations, HashMap<Ion.IonType,​HashSet<Integer>> iontypes, ArrayList<NeutralLoss> neutralLosses, boolean singleChargeSelected, boolean doubleChargeSelected, boolean moreThanTwoChargesSelected)
      Deprecated.
      used only in demo classes
      Filters the annotations and returns the annotations matching the currently selected types.
      Parameters:
      annotations - the annotations to be filtered, the annotations are assumed to have the following form: ion type + [ion number] + [charge] + [neutral loss]
      iontypes - the fragment ion types to include, assumed to be one of the Ion types, e.g, IonType.PeptideFragmentIon > PeptideFragmentIon.B_ION
      neutralLosses - list of neutral losses to display
      singleChargeSelected - if singly charged fragments are to be included
      doubleChargeSelected - if double charged fragments are to be included
      moreThanTwoChargesSelected - if fragments with more than two charges are to be included
      Returns:
      the filtered annotations
    • setIonColor

      public static void setIonColor​(Ion ion, Color color)
      Sets an annotation color for the given ion.
      Parameters:
      ion - the ion
      color - the new color
    • determineFragmentIonColor

      public static Color determineFragmentIonColor​(Ion ion, boolean isSpectrum)
      Returns the peak color to be used for the given peak label according to the color map. If not implemented returns the default color.
      Parameters:
      ion - the ion
      isSpectrum - if true, the special spectrum color is used for the y-ion
      Returns:
      the peak color
    • determineDefaultFragmentIonColor

      public static Color determineDefaultFragmentIonColor​(Ion ion, boolean isSpectrum)
      Returns the peak color to be used for the given peak label. The colors used are based on the color coding used in MascotDatfile.
      Parameters:
      ion - the ion
      isSpectrum - if true, the special spectrum color is used for the y-ion
      Returns:
      the peak color
    • determineFragmentIonColor

      public static Color determineFragmentIonColor​(String seriesLabel)
      Deprecated.
      use the method based on the Ion class instead
      Returns the color to use for the given fragment ion label.
      Parameters:
      seriesLabel - the series label
      Returns:
      the fragment ion color
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2. Fixed modifications are not annotated.
      Parameters:
      currentPeptide - the current peptide sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      mirrored - if true the annotation is for the mirrored spectrum
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Add reference areas annotating the de novo tags, using default alpha levels of 0.2. Fixed modifications are not annotated.
      Parameters:
      currentPeptide - the current peptide sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      mirrored - if true the annotation is for the mirrored spectrum
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
      Parameters:
      currentPeptide - the current peptide sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      excludeFixedModifications - are fixed modifications to be annotated?
      mirrored - if true the annotation is for the mirrored spectrum
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored)
      Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2. Fixed modifications are not annotated.
      Parameters:
      tag - the current tag sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      mirrored - if true the annotation is for the mirrored spectrum
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored)
      Add reference areas annotating the de novo tags, using default alpha levels of 0.2. Fixed modifications are not annotated.
      Parameters:
      tag - the current tag sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      mirrored - if true the annotation is for the mirrored spectrum
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored)
      Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
      Parameters:
      tag - the current tag sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      alphaLevels - the individual alpha levels, if set override forwardIonAlphaLevel and rewindIonAlphaLevel
      excludeFixedModifications - are fixed modifications to be annotated?
      mirrored - if true the annotation is for the mirrored spectrum
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Add reference areas annotating the de novo tags.
      Parameters:
      currentPeptide - the current peptide sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      alphaLevels - the individual alpha levels, if set override forwardIonAlphaLevel and rewindIonAlphaLevel
      excludeFixedModifications - are fixed modifications to be annotated?
      mirrored - if true the annotation is for the mirrored spectrum
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
      Add reference areas annotating the de novo tags.
      Parameters:
      currentPeptide - the current peptide sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showRewindTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      forwardIonAlphaLevel - alpha level of the forward ions
      rewindIonAlphaLevel - alpha level of the reverse ions
      alphaLevels - the individual alpha levels, if set override forwardIonAlphaLevel and rewindIonAlphaLevel
      excludeFixedModifications - are fixed modifications to be annotated?
      mirrored - if true the annotation is for the mirrored spectrum
      modificationParameters - the modification parameters
      sequenceProvider - a provider for the protein sequences
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
    • addAutomaticDeNovoSequencing

      public void addAutomaticDeNovoSequencing​(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored)
      Add reference areas annotating the de novo tags.
      Parameters:
      tag - the current tag sequence
      annotations - the current fragment ion annotations
      aForwardIon - the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_ION
      aRewindIon - the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_ION
      aDeNovoCharge - the de novo sequencing charge
      showForwardTags - if true, the forward de novo sequencing tags are displayed
      showReverseTags - if true, the reverse de novo sequencing tags are displayed
      forwardIonPercentHeight - the percent height of the forward ion annotation [0-1]
      rewindIonPercentHeight - the percent height of the reverse ion annotation [0-1]
      forwardIonAlphaLevel - alpha level of the forward ions
      rewindIonAlphaLevel - alpha level of the reverse ions
      alphaLevels - the individual alpha levels, if set override forwardIonAlphaLevel and rewindIonAlphaLevel
      excludeFixedModifications - are fixed modifications to be annotated?
      mirrored - if true the annotation is for the mirrored spectrum