public class SpectrumPanel extends GraphicsPanel
GraphicsPanel.DrawingStyle, GraphicsPanel.GraphicsPanelType
JPanel.AccessibleJPanel
JComponent.AccessibleJComponent
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Constructor and Description |
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SpectrumPanel(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.
|
Modifier and Type | Method and 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,
ArrayList<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(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
void |
addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<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(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
void |
addAutomaticDeNovoSequencing(Tag tag,
ArrayList<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,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
addAutomaticDeNovoSequencing(Tag tag,
ArrayList<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,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
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void |
addMirroredSpectrum(double[] aXAxisData,
double[] aYAxisData,
double aPrecursorMZ,
String aPrecursorCharge,
String aFileName,
boolean aProfileMode,
Color aSpectrumPeakColor,
Color aSpectrumProfileModeLineColor)
Add a mirrored spectrum (or chromatogram).
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static Color |
determineColorOfPeak(String peakLabel)
Deprecated.
it is advised to use methods based on the ion type rather
than on the peak label
|
static Color |
determineDefaultFragmentIonColor(Ion ion,
boolean isSpectrum)
Returns the peak color to be used for the given peak label.
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static 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 Color |
determineFragmentIonColor(String seriesLabel)
Deprecated.
use the method based on the Ion class instead
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static Vector<SpectrumAnnotation> |
filterAnnotations(Vector<SpectrumAnnotation> annotations,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
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,
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 |
setSpectrumPeakColor(Color aSpectrumPeakColor)
Set the default spectrum peak color.
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void |
setSpectrumProfileModeLineColor(Color aSpectrumProfileModeLineColor)
Set the default spectrum profile mode color.
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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, 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
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, 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
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, 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, GraphicsPanel.DrawingStyle 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
- the drawing style to use.aEnableInteraction
- boolean that specifies whether user-derived
events should be caught and dealt with.public SpectrumPanel(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, 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
- 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.public SpectrumPanel(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, 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
- 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 panelpublic SpectrumPanel(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, 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
- 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 panelpublic SpectrumPanel(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, 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
- 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 spectrumpublic SpectrumPanel(SpectrumFile aSpecFile, GraphicsPanel.DrawingStyle aDrawStyle, boolean aEnableInteraction, 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
- 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 modepublic SpectrumPanel(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, 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, String aPrecursorCharge, 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, String aPrecursorCharge, 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, String aPrecursorCharge, 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, String aPrecursorCharge, 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, String aPrecursorCharge, 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 addMirroredSpectrum(double[] aXAxisData, double[] aYAxisData, double aPrecursorMZ, String aPrecursorCharge, String aFileName, boolean aProfileMode, Color aSpectrumPeakColor, Color aSpectrumProfileModeLineColor)
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 colorpublic void addAdditionalDataset(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, 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 addAdditionalMirroredDataset(double[] aXAxisData, double[] aYAxisData, Color dataPointAndLineColor, 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 setSpectrumPeakColor(Color aSpectrumPeakColor)
aSpectrumPeakColor
- the color to setpublic void setSpectrumProfileModeLineColor(Color aSpectrumProfileModeLineColor)
aSpectrumProfileModeLineColor
- the color to setpublic 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 Color determineColorOfPeak(String peakLabel)
peakLabel
- the peak labelpublic static Vector<SpectrumAnnotation> filterAnnotations(Vector<SpectrumAnnotation> annotations, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, 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, Color color)
ion
- the ioncolor
- the new colorpublic static Color determineFragmentIonColor(Ion ion, boolean isSpectrum)
ion
- the ionisSpectrum
- if true, the special spectrum color is used for the
y-ionpublic static Color determineDefaultFragmentIonColor(Ion ion, boolean isSpectrum)
ion
- the ionisSpectrum
- if true, the special spectrum color is used for the
y-ionpublic static Color determineFragmentIonColor(String seriesLabel)
seriesLabel
- the series labelpublic void addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored)
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 spectrumpublic void addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored)
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 spectrumpublic void addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean excludeFixedPtms, boolean mirrored)
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]excludeFixedPtms
- are fixed PTMs to be annotated?mirrored
- if true the annotation is for the mirrored spectrumpublic void addAutomaticDeNovoSequencing(Tag tag, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored)
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 spectrumpublic void addAutomaticDeNovoSequencing(Tag tag, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored)
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 spectrumpublic void addAutomaticDeNovoSequencing(Tag tag, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedPtms, boolean mirrored)
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 rewindIonAlphaLevelexcludeFixedPtms
- are fixed PTMs to be annotated?mirrored
- if true the annotation is for the mirrored spectrumpublic void addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedPtms, boolean mirrored)
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 rewindIonAlphaLevelexcludeFixedPtms
- are fixed PTMs to be annotated?mirrored
- if true the annotation is for the mirrored spectrumpublic void addAutomaticDeNovoSequencing(Peptide currentPeptide, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedPtms, boolean mirrored)
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 rewindIonAlphaLevelexcludeFixedPtms
- are fixed PTMs to be annotated?mirrored
- if true the annotation is for the mirrored spectrumpublic void addAutomaticDeNovoSequencing(Tag tag, ArrayList<IonMatch> annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedPtms, boolean mirrored)
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 rewindIonAlphaLevelexcludeFixedPtms
- are fixed PTMs to be annotated?mirrored
- if true the annotation is for the mirrored spectrumCopyright © 2016. All rights reserved.