Package com.compomics.util.gui.spectrum
Class IsotopicDistributionPanel
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.IsotopicDistributionPanel
- All Implemented Interfaces:
ImageObserver
,MenuContainer
,Serializable
,Accessible
public class IsotopicDistributionPanel extends GraphicsPanel
This class provides a JPanel that can display a peptide isotopic distribution.
- Version:
- $Id$
- Author:
- Harald Barsnes, Niklaas Colaert, Lennart Martens
- 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 IsotopicDistributionPanel()
Empty default constructorIsotopicDistributionPanel(String peptideSequence, Integer peptideCharge, boolean profileMode, int labelDifference)
This constructor creates an IsotopicDistributionPanel based on the passed parameters. -
Method Summary
Modifier and Type Method Description 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.ArrayList<AASequenceImpl>
getPeptideSequences()
Get the set of peptide sequences.boolean
isElement(String lElement)
Method that checks if a given string is an element we can calculate an isotopic distribution forMethods 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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IsotopicDistributionPanel
public IsotopicDistributionPanel()Empty default constructor -
IsotopicDistributionPanel
public IsotopicDistributionPanel(String peptideSequence, Integer peptideCharge, boolean profileMode, int labelDifference) throws IOExceptionThis constructor creates an IsotopicDistributionPanel based on the passed parameters.- Parameters:
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 label- Throws:
IOException
- if an IOException occurs
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Method Details
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addAdditionalDataset
public void addAdditionalDataset(String peptideSequence, Integer peptideCharge, Color dataPointAndLineColor, Color areaUnderCurveColor, int labelDifference) throws IOExceptionAdds an additional isotopic distribution dataset to be displayed in the same panel. Remember to use different colors for the different datasets.- Parameters:
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 label- Throws:
IOException
- if an IOException occurs
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isElement
Method that checks if a given string is an element we can calculate an isotopic distribution for- Parameters:
lElement
- String with the element to check- Returns:
- boolean that indicates if we can use this element
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getPeptideSequences
Get the set of peptide sequences.- Returns:
- the peptideSequences
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