Package com.compomics.util.gui.spectrum
Class SpectrumPanel
java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
com.compomics.util.gui.spectrum.GraphicsPanel
com.compomics.util.gui.spectrum.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
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Nested Class Summary
Nested classes/interfaces inherited from class com.compomics.util.gui.spectrum.GraphicsPanel
GraphicsPanel.DrawingStyle, GraphicsPanel.GraphicsPanelType
Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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Field Summary
Fields inherited from class com.compomics.util.gui.spectrum.GraphicsPanel
alphaLevel, ANNOTATED_STATUS, annotateHighestPeak, currentGraphicsPanelType, currentPadding, dataSetCounter, dataSetCounterMirroredSpectra, deltaMassWindow, iAnnotations, iAnnotationsMirroredSpectra, iAnnotationYAxisThreshold, iAreaUnderCurveColor, iAreaUnderCurveColorMirroredSpectra, iClicked, iClickedDataSetIndex, iClickedDataSetIndexMirrored, iClickedIndex, iClickedIndexMirrored, iClickedList, iClickedListDatasetIndices, iClickedListDatasetIndicesMirrored, iClickedListMirrored, iClickedMirrored, iCurrentDrawStyle, iDataPointAndLineColor, iDataPointAndLineColorMirroredSpectra, iDotRadius, iDragged, iDragXLoc, iEndXLoc, iFilename, iFilenameColor, iFilenameMirrorredSpectrum, iHighLight, iHighLightDatasetIndex, iHighLightDatasetIndexMirrored, iHighLightIndex, iHighLightIndexMirrored, iHighLightMirrored, iKnownMassDeltas, iMinDrag, iMSLevel, INTERACTIVE_STATUS, iPointDetectionTolerance, iPointSize, iPrecursorCharge, iPrecursorChargeMirorredSpectrum, iPrecursorMZ, iPrecursorMZMirroredSpectrum, iSpecPanelListeners, iStartXLoc, iStartYLoc, iStoredSequence, iStoredSequenceDatasetIndices, iStoredSequenceDatasetIndicesMirrored, iStoredSequenceMirrored, iTopPadding, iXAxisData, iXAxisDataInPixels, iXAxisDataInPixelsMirroredSpectrum, iXAxisDataMirroredSpectrum, iXAxisLabel, iXAxisMax, iXAxisMin, iXAxisStartAtZero, iXPadding, iXScaleUnit, iXUnit, iYAxisData, iYAxisDataInPixels, iYAxisDataInPixelsMirroredSpectrum, iYAxisDataMirroredSpectrum, iYAxisLabel, iYAxisMax, iYAxisMin, iYScaleUnit, iYUnit, maxPadding, miniature, padding, showAllPeaks, showFileName, showPrecursorDetails, showResolution, xAxisZoomRangeLowerValue, xAxisZoomRangeUpperValue, xTagCount, yAxisZoomExcludesBackgroundPeaks, yDataIsPositive, yTagCount
Fields inherited from class javax.swing.JComponent
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
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Constructor Summary
Constructors Constructor Description SpectrumPanel()
Empty default constructorSpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName)
This constructor creates a SpectrumPanel based on the passed parameters.SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, boolean aShowFileName)
This constructor creates a SpectrumPanel based on the passed parameters.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.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.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.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.SpectrumPanel(SpectrumFile aSpecFile)
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile as an interactive lines plot.SpectrumPanel(SpectrumFile aSpecFile, boolean aEnableInteraction)
This constructor creates a SpectrumPanel based on the spectrum information in the specified SpectrumFile as a line plot.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.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.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.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.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.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. -
Method Summary
Modifier and Type Method Description void
addAdditionalDataset(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)
Adds an additional spectrum dataset to be displayed in the same Spectrum Panel.void
addAdditionalMirroredDataset(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, Color areaUnderCurveColor)
Adds an additional mirrored spectrum dataset to be displayed in the same Spectrum Panel.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.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.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.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.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.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.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.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.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.void
addMirroredSpectrum(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, boolean aProfileMode, Color aSpectrumPeakColor, Color aSpectrumProfileModeLineColor)
Add a mirrored spectrum (or chromatogram).static Color
determineColorOfPeak(String peakLabel)
Deprecated.it is advised to use methods based on the ion type rather than on the peak labelstatic Color
determineDefaultFragmentIonColor(Ion ion, boolean isSpectrum)
Returns the peak color to be used for the given peak label.static Color
determineFragmentIonColor(Ion ion, boolean isSpectrum)
Returns the peak color to be used for the given peak label according to the color map.static Color
determineFragmentIonColor(String seriesLabel)
Deprecated.use the method based on the Ion class insteadstatic 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 classesstatic void
setIonColor(Ion ion, Color color)
Sets an annotation color for the given ion.void
setProfileMode(boolean aProfileMode)
Change the drawing type of the spectrum.void
setSpectrumFile(SpectrumFile aSpecFile)
This method initializes a SpectrumPanel based on the spectrum information in the specified SpectrumFile.void
setSpectrumPeakColor(Color aSpectrumPeakColor)
Set the default spectrum peak color.void
setSpectrumProfileModeLineColor(Color aSpectrumProfileModeLineColor)
Set the default spectrum profile mode color.void
showAnnotatedPeaksOnly(boolean aAnnotatedPeaks)
If true only the annotated peaks will be drawn.Methods inherited from class com.compomics.util.gui.spectrum.GraphicsPanel
addListeners, addReferenceAreaXAxis, addReferenceAreaYAxis, addSpectrumPanelListener, annotate, annotatePeaks, drawAxes, drawDaisyChain, drawFilledPolygon, drawMeasurementLine, drawMirroredPeaks, drawPeaks, drawXAxisReferenceAreas, drawXTags, drawYAxisReferenceAreas, drawYTags, dropDottedLine, findDeltaMassMatches, getAllReferenceAreasXAxis, getAllReferenceAreasYAxis, getAlphaLevel, getAreaUnderCurveColors, getBackgroundPeakWidth, getDeltaMassWindow, getiXAxisMax, getiXAxisMin, getiYAxisMax, getiYAxisMin, getKnownMassDeltas, getMaxPadding, getMaxXAxisValue, getMinXAxisValue, getPeakWaterMarkColor, getPeakWidth, getXAxisData, getXAxisZoomRangeLowerValue, getXAxisZoomRangeUpperValue, getYAxisData, highLight, highlightClicked, highLightPeak, isAnnotateHighestPeak, isMiniature, isSubscriptAnnotationNumbers, paint, processMirroredXAndYData, processXAndYData, removeAllReferenceAreasXAxis, removeAllReferenceAreasYAxis, removeReferenceAreaXAxis, removeReferenceAreaYAxis, rescale, rescale, setAlphaLevel, setAnnotateHighestPeak, setAnnotations, setAnnotations, setAnnotationsMirrored, setAnnotationsMirrored, setAnnotationYAxisThreshold, setAreaUnderCurveColor, setBackgroundPeakWidth, setDataPointAndLineColor, setDeltaMassWindow, setFilenameColor, setiXAxisMax, setiXAxisMin, setiYAxisMax, setiYAxisMin, setKnownMassDeltas, setMaxPadding, setMiniature, setPeakWaterMarkColor, setPeakWidth, setScientificXAxis, setScientificXAxis, setScientificYAxis, setScientificYAxis, setShowPrecursorDetails, setShowResolution, setSubscriptAnnotationNumbers, setUseMassDeltaCombinations, setXAxisStartAtZero, setYAxisZoomExcludesBackgroundPeaks, setYDataIsPositive, showPrecursorDetails, showResolution, useMassDeltaCombinations, yAxisZoomOnlyExcludesBackgroundPeaks, yDataIsPositive
Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTree
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle
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Constructor Details
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SpectrumPanel
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.
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SpectrumPanel
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.
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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.
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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.
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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
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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 panelaShowPrecursorDetails
- boolean that specifies if the precursor details should be shown in the panelaShowResolution
- boolean that specifies if the resolution should be shown in the panel
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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 panelaShowPrecursorDetails
- boolean that specifies if the precursor details should be shown in the panelaShowResolution
- boolean that specifies if the resolution should be shown in the panelaMSLevel
- int with the ms level for the spectrum
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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 panelaShowPrecursorDetails
- boolean that specifies if the precursor details should be shown in the panelaShowResolution
- boolean that specifies if the resolution should be shown in the panelaMSLevel
- int with the ms level for the spectrum, set to 0 if ms level is unknownaProfileMode
- boolean if set to true the spectrum will be drawn in profile mode
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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.
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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.
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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.
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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 panelaShowPrecursorDetails
- boolean that specifies if the precursor details should be shown in the panelaShowResolution
- boolean that specifies if the resolution should be shown in the panel
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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 panelaShowPrecursorDetails
- boolean that specifies if the precursor details should be shown in the panelaShowResolution
- boolean that specifies if the resolution should be shown in the panelaMSLevel
- int with the ms level for the spectrum, set to 0 if ms level is unknown
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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 panelaShowPrecursorDetails
- boolean that specifies if the precursor details should be shown in the panelaShowResolution
- boolean that specifies if the resolution should be shown in the panelaMSLevel
- int with the ms level for the spectrum, set to 0 if ms level is unknownaProfileMode
- boolean if set to true the spectrum will be drawn in profile mode
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Method Details
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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 dataaYAxisData
- the y axis dataaPrecursorMZ
- the precursor m/zaPrecursorCharge
- the precursor chargeaFileName
- the file nameaProfileMode
- if the spectrum is to be drawn in profile modeaSpectrumPeakColor
- the spectrum peak coloraSpectrumProfileModeLineColor
- the spectrum profile mode line color
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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 valuesdataPointAndLineColor
- the color to use for the data points and linesareaUnderCurveColor
- the color to use for the area under the curve
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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 valuesdataPointAndLineColor
- the color to use for the data points and linesareaUnderCurveColor
- the color to use for the area under the curve
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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
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setSpectrumPeakColor
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
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setSpectrumProfileModeLineColor
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
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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
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setSpectrumFile
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.
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determineColorOfPeak
Deprecated.it is advised to use methods based on the ion type rather than on the peak labelReturns 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
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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 classesFilters 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_IONneutralLosses
- list of neutral losses to displaysingleChargeSelected
- if singly charged fragments are to be includeddoubleChargeSelected
- if double charged fragments are to be includedmoreThanTwoChargesSelected
- if fragments with more than two charges are to be included- Returns:
- the filtered annotations
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setIonColor
Sets an annotation color for the given ion.- Parameters:
ion
- the ioncolor
- the new color
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determineFragmentIonColor
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 ionisSpectrum
- if true, the special spectrum color is used for the y-ion- Returns:
- the peak color
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determineDefaultFragmentIonColor
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 ionisSpectrum
- if true, the special spectrum color is used for the y-ion- Returns:
- the peak color
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determineFragmentIonColor
Deprecated.use the method based on the Ion class insteadReturns the color to use for the given fragment ion label.- Parameters:
seriesLabel
- the series label- Returns:
- the fragment ion color
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedmirrored
- if true the annotation is for the mirrored spectrummodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mapping
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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 spectrummodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mapping
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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 spectrummodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mapping
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedmirrored
- if true the annotation is for the mirrored spectrum
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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 rewindIonAlphaLevelexcludeFixedModifications
- are fixed modifications to be annotated?mirrored
- if true the annotation is for the mirrored spectrum
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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 rewindIonAlphaLevelexcludeFixedModifications
- are fixed modifications to be annotated?mirrored
- if true the annotation is for the mirrored spectrummodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mapping
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowRewindTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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 ionsrewindIonAlphaLevel
- alpha level of the reverse ionsalphaLevels
- the individual alpha levels, if set override forwardIonAlphaLevel and rewindIonAlphaLevelexcludeFixedModifications
- are fixed modifications to be annotated?mirrored
- if true the annotation is for the mirrored spectrummodificationParameters
- the modification parameterssequenceProvider
- a provider for the protein sequencesmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mapping
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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 sequenceannotations
- the current fragment ion annotationsaForwardIon
- the forward de novo sequencing fragment ion type, i.e., PeptideFragmentIon.A_ION, PeptideFragmentIon.B_ION or PeptideFragmentIon.C_IONaRewindIon
- the reverse de novo sequencing fragment ion type, i.e., PeptideFragmentIon.X_ION, PeptideFragmentIon.Y_ION or PeptideFragmentIon.Z_IONaDeNovoCharge
- the de novo sequencing chargeshowForwardTags
- if true, the forward de novo sequencing tags are displayedshowReverseTags
- if true, the reverse de novo sequencing tags are displayedforwardIonPercentHeight
- 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 ionsrewindIonAlphaLevel
- alpha level of the reverse ionsalphaLevels
- the individual alpha levels, if set override forwardIonAlphaLevel and rewindIonAlphaLevelexcludeFixedModifications
- are fixed modifications to be annotated?mirrored
- if true the annotation is for the mirrored spectrum
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