public class IsotopicDistributionPanel extends GraphicsPanel
GraphicsPanel.DrawingStyle, GraphicsPanel.GraphicsPanelTypeJPanel.AccessibleJPanelJComponent.AccessibleJComponentContainer.AccessibleAWTContainerComponent.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategyalphaLevel, 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, yTagCountlistenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOWaccessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENTABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH| Constructor and Description |
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IsotopicDistributionPanel(String peptideSequence,
Integer peptideCharge,
boolean profileMode,
int labelDifference)
This constructor creates an IsotopicDistributionPanel based on the passed parameters.
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| Modifier and Type | Method and Description |
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void |
addAdditionalDataset(String peptideSequence,
Integer peptideCharge,
Color dataPointAndLineColor,
Color areaUnderCurveColor,
int labelDifference)
Adds an additional isotopic distribution dataset to be displayed in the same
panel.
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ArrayList<AASequenceImpl> |
getPeptideSequences()
Get the set of peptide sequences.
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boolean |
isElement(String lElement)
Method that checks if a given string is an element we can calculate an isotopic distribution for
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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, yDataIsPositivegetAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUIaddAncestorListener, 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, updateadd, 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, validateTreeaction, 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, transferFocusUpCyclepublic IsotopicDistributionPanel(String peptideSequence, Integer peptideCharge, boolean profileMode, int labelDifference) throws IOException
peptideSequence - the peptide sequence to display the isotopic distribution forpeptideCharge - the charge of the peptideprofileMode - if true the peaks will be showed in a profile like mode where
support peaks are added in front of and after the real peak
(note that this is unlike the profile modes of the other graphics
panels)labelDifference - the number of neutrons to add due to the labelIOException - if an IOException occurspublic void addAdditionalDataset(String peptideSequence, Integer peptideCharge, Color dataPointAndLineColor, Color areaUnderCurveColor, int labelDifference) throws IOException
peptideSequence - the peptide sequence to display the isotopic distribution forpeptideCharge - the charge of the peptidedataPointAndLineColor - the color to use for the data points and linesareaUnderCurveColor - the color to use for the area under the curvelabelDifference - the number of neutrons to add due to the labelIOException - if an IOException occurspublic boolean isElement(String lElement)
lElement - String with the element to checkpublic ArrayList<AASequenceImpl> getPeptideSequences()
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