public class SpectrumPanel extends GraphicsPanel
GraphicsPanel.GraphicsPanelType
javax.swing.JPanel.AccessibleJPanel
javax.swing.JComponent.AccessibleJComponent
alphaLevel, ANNOTATED_STATUS, currentGraphicsPanelType, currentPadding, dataSetCounter, deltaMassWindow, DOTS, iAnnotations, iAnnotationYAxisThreshold, iAreaUnderCurveColor, iClicked, iClickedDataSetIndex, iClickedIndex, iClickedList, iClickedListDatasetIndices, iDataPointAndLineColor, iDotRadius, iDragged, iDragXLoc, iDrawStyle, iEndXLoc, iFilename, iFilenameColor, iHighLight, iHighLightDatasetIndex, iHighLightIndex, iKnownMassDeltas, iMinDrag, iMSLevel, INTERACTIVE_STATUS, iPointDetectionTolerance, iPointSize, iPrecursorCharge, iPrecursorMZ, iSpecPanelListeners, iStartXLoc, iStartYLoc, iStoredSequence, iStoredSequenceDatasetIndices, iTopPadding, iXAxisData, iXAxisDataInPixels, iXAxisLabel, iXAxisMax, iXAxisMin, iXAxisStartAtZero, iXPadding, iXScaleUnit, iXUnit, iYAxisData, iYAxisDataInPixels, iYAxisLabel, iYAxisMax, iYAxisMin, iYScaleUnit, iYUnit, LINES, maxPadding, miniature, padding, showAllPeaks, showFileName, showPrecursorDetails, showResolution, xAxisZoomRangeLowerValue, xAxisZoomRangeUpperValue, xTagCount, yAxisZoomExcludesBackgroundPeaks, yDataIsPositive, yTagCount
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
Constructor and Description |
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SpectrumPanel(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
java.lang.String aPrecursorCharge,
java.lang.String aFileName)
This constructor creates a SpectrumPanel based on the passed parameters.
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SpectrumPanel(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
java.lang.String aPrecursorCharge,
java.lang.String aFileName,
boolean aShowFileName)
This constructor creates a SpectrumPanel based on the passed parameters.
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SpectrumPanel(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
java.lang.String aPrecursorCharge,
java.lang.String aFileName,
int aMaxPadding,
boolean aShowFileName)
This constructor creates a SpectrumPanel based on the passed parameters.
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SpectrumPanel(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
java.lang.String aPrecursorCharge,
java.lang.String aFileName,
int aMaxPadding,
boolean aShowFileName,
boolean aShowPrecursorDetails,
boolean aShowResolution)
This constructor creates a SpectrumPanel based on the passed parameters.
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SpectrumPanel(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
java.lang.String aPrecursorCharge,
java.lang.String aFileName,
int aMaxPadding,
boolean aShowFileName,
boolean aShowPrecursorDetails,
boolean aShowResolution,
int aMSLevel)
This constructor creates a SpectrumPanel based on the passed parameters.
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SpectrumPanel(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
java.lang.String aPrecursorCharge,
java.lang.String aFileName,
int aMaxPadding,
boolean aShowFileName,
boolean aShowPrecursorDetails,
boolean aShowResolution,
int aMSLevel,
boolean aProfileMode)
This constructor creates a SpectrumPanel based on the passed parameters.
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SpectrumPanel(SpectrumFile aSpecFile)
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile as an interactive lines plot.
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SpectrumPanel(SpectrumFile aSpecFile,
boolean aEnableInteraction)
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile as a line plot.
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SpectrumPanel(SpectrumFile aSpecFile,
int aDrawStyle,
boolean aEnableInteraction)
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
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SpectrumPanel(SpectrumFile aSpecFile,
int aDrawStyle,
boolean aEnableInteraction,
java.awt.Color aSpectrumFilenameColor)
This constructor creates a SpectrumPanel based on the spectrum
information in the specified SpectrumFile with the specified drawing
style.
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SpectrumPanel(SpectrumFile aSpecFile,
int aDrawStyle,
boolean aEnableInteraction,
java.awt.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.
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SpectrumPanel(SpectrumFile aSpecFile,
int aDrawStyle,
boolean aEnableInteraction,
java.awt.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.
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SpectrumPanel(SpectrumFile aSpecFile,
int aDrawStyle,
boolean aEnableInteraction,
java.awt.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.
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SpectrumPanel(SpectrumFile aSpecFile,
int aDrawStyle,
boolean aEnableInteraction,
java.awt.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.
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Modifier and Type | Method and Description |
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void |
addAdditionalDataset(double[] aXAxisData,
double[] aYAxisData,
java.awt.Color dataPointAndLineColor,
java.awt.Color areaUnderCurveColor)
Adds an additional spectrum dataset to be displayed in the same Spectrum
Panel.
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void |
addAutomaticDeNovoSequencing(Peptide currentPeptide,
java.util.ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags)
Add reference areas annotating the de novo tags.
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static java.awt.Color |
determineColorOfPeak(java.lang.String peakLabel)
Deprecated.
it is advised to use methods based on the ion type rather
than on the peak label
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static java.awt.Color |
determineDefaultFragmentIonColor(Ion ion,
boolean isSpectrum)
Returns the peak color to be used for the given peak label.
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static java.awt.Color |
determineFragmentIonColor(Ion ion,
boolean isSpectrum)
Returns the peak color to be used for the given peak label according to
the color map.
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static java.awt.Color |
determineFragmentIonColor(java.lang.String seriesLabel)
Deprecated.
use the method based on the Ion class instead
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static java.util.Vector<DefaultSpectrumAnnotation> |
filterAnnotations(java.util.Vector<DefaultSpectrumAnnotation> annotations,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated.
don't use method based on the peak labels but on the data
type
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static void |
setIonColor(Ion ion,
java.awt.Color color)
Sets an annotation color for the given ion.
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void |
setProfileMode(boolean aProfileMode)
Change the drawing type of the spectrum.
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void |
setSpectrumFile(SpectrumFile aSpecFile)
This method initializes a SpectrumPanel based on the spectrum information
in the specified SpectrumFile.
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void |
showAnnotatedPeaksOnly(boolean aAnnotatedPeaks)
If true only the annotated peaks will be drawn.
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addListeners, addReferenceAreaXAxis, addReferenceAreaYAxis, addSpectrumPanelListener, annotate, drawAxes, drawFilledPolygon, drawMeasurementLine, drawPeaks, drawXAxisReferenceAreas, drawXTags, drawYAxisReferenceAreas, drawYTags, dropDottedLine, findDeltaMassMatches, getAllReferenceAreasXAxis, getAllReferenceAreasYAxis, getAlphaLevel, getAreaUnderCurveColors, getBackgroundPeakWidth, getDeltaMassWindow, getKnownMassDeltas, getMaxPadding, getMaxXAxisValue, getMinXAxisValue, getPeakWaterMarkColor, getPeakWidth, getXAxisData, getXAxisZoomRangeLowerValue, getXAxisZoomRangeUpperValue, getYAxisData, highLight, highlightClicked, highLightPeak, isMiniature, isSubscriptAnnotationNumbers, paint, processXAndYData, removeAllReferenceAreasXAxis, removeAllReferenceAreasYAxis, removeReferenceAreaXAxis, removeReferenceAreaYAxis, rescale, rescale, setAlphaLevel, setAnnotations, setAnnotationYAxisThreshold, setAreaUnderCurveColor, setBackgroundPeakWidth, setDataPointAndLineColor, setDeltaMassWindow, setFilenameColor, setKnownMassDeltas, setMaxPadding, setMiniature, setPeakWaterMarkColor, setPeakWidth, setScientificXAxis, setScientificXAxis, setScientificYAxis, setScientificYAxis, setShowPrecursorDetails, setShowResolution, setSubscriptAnnotationNumbers, setUseMassDeltaCombinations, setXAxisStartAtZero, setYAxisZoomExcludesBackgroundPeaks, setYDataIsPositive, showPrecursorDetails, showResolution, useMassDeltaCombinations, yAxisZoomOnlyExcludesBackgroundPeaks, yDataIsPositive
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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, 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
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
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, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, 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, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle
public SpectrumPanel(SpectrumFile aSpecFile)
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.public SpectrumPanel(SpectrumFile aSpecFile, boolean aEnableInteraction)
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.public SpectrumPanel(SpectrumFile aSpecFile, int aDrawStyle, boolean aEnableInteraction)
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
- int with the drawing style to use. It should be one of
the constants defined on this class.aEnableInteraction
- boolean that specifies whether user-derived
events should be caught and dealt with.public SpectrumPanel(SpectrumFile aSpecFile, int aDrawStyle, boolean aEnableInteraction, java.awt.Color aSpectrumFilenameColor)
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
- int with the drawing style to use. It should be one of
the constants defined on this class.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.public SpectrumPanel(SpectrumFile aSpecFile, int aDrawStyle, boolean aEnableInteraction, java.awt.Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName)
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
- int with the drawing style to use. It should be one of
the constants defined on this class.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 panelpublic SpectrumPanel(SpectrumFile aSpecFile, int aDrawStyle, boolean aEnableInteraction, java.awt.Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution)
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
- int with the drawing style to use. It should be one of
the constants defined on this class.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 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 panelpublic SpectrumPanel(SpectrumFile aSpecFile, int aDrawStyle, boolean aEnableInteraction, java.awt.Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel)
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
- int with the drawing style to use. It should be one of
the constants defined on this class.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 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 spectrumpublic SpectrumPanel(SpectrumFile aSpecFile, int aDrawStyle, boolean aEnableInteraction, java.awt.Color aSpectrumFilenameColor, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel, boolean aProfileMode)
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
- int with the drawing style to use. It should be one of
the constants defined on this class.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 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 modepublic SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, java.lang.String aPrecursorCharge, java.lang.String aFileName)
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.public SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, java.lang.String aPrecursorCharge, java.lang.String aFileName, boolean aShowFileName)
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.public SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, java.lang.String aPrecursorCharge, java.lang.String aFileName, int aMaxPadding, boolean aShowFileName)
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.public SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, java.lang.String aPrecursorCharge, java.lang.String aFileName, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution)
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 panelpublic SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, java.lang.String aPrecursorCharge, java.lang.String aFileName, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel)
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 unknownpublic SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, java.lang.String aPrecursorCharge, java.lang.String aFileName, int aMaxPadding, boolean aShowFileName, boolean aShowPrecursorDetails, boolean aShowResolution, int aMSLevel, boolean aProfileMode)
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 modepublic void addAdditionalDataset(double[] aXAxisData, double[] aYAxisData, java.awt.Color dataPointAndLineColor, java.awt.Color areaUnderCurveColor)
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 curvepublic void setProfileMode(boolean aProfileMode)
aProfileMode
- if true, the spectrum is drawn in profile modepublic void showAnnotatedPeaksOnly(boolean aAnnotatedPeaks)
aAnnotatedPeaks
- if true only the annotated peaks will be drawnpublic void setSpectrumFile(SpectrumFile aSpecFile)
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.public static java.awt.Color determineColorOfPeak(java.lang.String peakLabel)
peakLabel
- public static java.util.Vector<DefaultSpectrumAnnotation> filterAnnotations(java.util.Vector<DefaultSpectrumAnnotation> annotations, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<NeutralLoss> neutralLosses, boolean singleChargeSelected, boolean doubleChargeSelected, boolean moreThanTwoChargesSelected)
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 includedpublic static void setIonColor(Ion ion, java.awt.Color color)
ion
- the ioncolor
- the new colorpublic static java.awt.Color determineFragmentIonColor(Ion ion, boolean isSpectrum)
ion
- the ionisSpectrum
- if true, the special spectrum color is used for the
y-ionpublic static java.awt.Color determineDefaultFragmentIonColor(Ion ion, boolean isSpectrum)
ion
- the ionisSpectrum
- if true, the special spectrum color is used for the
y-ionpublic static java.awt.Color determineFragmentIonColor(java.lang.String seriesLabel)
seriesLabel
- the series labelpublic void addAutomaticDeNovoSequencing(Peptide currentPeptide, java.util.ArrayList<IonMatch> annotations, int aForwardIon, int aReverseIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags)
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_IONaReverseIon
- 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
displayedCopyright © 2013. All Rights Reserved.