Package com.compomics.util.gui.spectrum
Class MassErrorBubblePlot
java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
com.compomics.util.gui.spectrum.MassErrorBubblePlot
- All Implemented Interfaces:
ImageObserver
,MenuContainer
,Serializable
,Accessible
public class MassErrorBubblePlot extends JPanel
Creates a MassErrorBubblePlot displaying the mz values vs the mass error with
the intensity as the size of the bubbles.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Nested Class Summary
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 Modifier and Type Field Description static float
DEFAULT_NON_VISIBLE_MARKER_ALPHA
The default non-visible alpha level.static float
DEFAULT_VISIBLE_MARKER_ALPHA
The default visible alpha level.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 MassErrorBubblePlot()
Empty default constructorMassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<IonMatch[]> annotations, ArrayList<Spectrum> currentSpectra, double massTolerance, boolean fragmentIonLabels, boolean addMarkers)
Creates a new MassErrorBubblePlot.MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<IonMatch[]> annotations, ArrayList<Spectrum> currentSpectra, double massTolerance, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
Creates a new MassErrorBubblePlot.MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<IonMatch[]> annotations, ArrayList<Spectrum> currentSpectra, double massTolerance, double bubbleScale, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
Creates a new MassErrorBubblePlot. -
Method Summary
Modifier and Type Method Description static void
addFragmentIonTypeMarkers(HashMap<IonMatch,ArrayList<XYZDataPoint>> data, org.jfree.chart.JFreeChart chart, boolean showMarkers)
Adds interval markers for all the fragment ion types.org.jfree.data.xy.DefaultXYZDataset
addXYZDataSeries(HashMap<IonMatch,ArrayList<XYZDataPoint>> data)
Adds the provided data series to an XYZ data set.org.jfree.chart.ChartPanel
getChartPanel()
Returns the chart panel.int
getNumberOfDataPointsInPlot()
Returns the current number of data points in the mass error plot.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, paint, 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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Field Details
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DEFAULT_VISIBLE_MARKER_ALPHA
public static final float DEFAULT_VISIBLE_MARKER_ALPHAThe default visible alpha level.- See Also:
- Constant Field Values
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DEFAULT_NON_VISIBLE_MARKER_ALPHA
public static final float DEFAULT_NON_VISIBLE_MARKER_ALPHAThe default non-visible alpha level.- See Also:
- Constant Field Values
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Constructor Details
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MassErrorBubblePlot
public MassErrorBubblePlot()Empty default constructor -
MassErrorBubblePlot
public MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<IonMatch[]> annotations, ArrayList<Spectrum> currentSpectra, double massTolerance, boolean fragmentIonLabels, boolean addMarkers)Creates a new MassErrorBubblePlot.- Parameters:
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentSpectra
- the current spectramassTolerance
- the mass error tolerancefragmentIonLabels
- if true, the fragment ion type is used as the data series key, otherwise the psm index is usedaddMarkers
- if true interval markers for the fragment ions will be shown
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MassErrorBubblePlot
public MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<IonMatch[]> annotations, ArrayList<Spectrum> currentSpectra, double massTolerance, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)Creates a new MassErrorBubblePlot.- Parameters:
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentSpectra
- the current spectramassTolerance
- the mass error tolerancefragmentIonLabels
- if true, the fragment ion type is used as the data series key, otherwise the psm index is usedaddMarkers
- if true interval markers for the fragment ions will be shownuseRelativeError
- if true the relative error (ppm) is used instead of the absolute error (Da)
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MassErrorBubblePlot
public MassErrorBubblePlot(ArrayList<String> dataIndexes, ArrayList<IonMatch[]> annotations, ArrayList<Spectrum> currentSpectra, double massTolerance, double bubbleScale, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)Creates a new MassErrorBubblePlot.- Parameters:
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentSpectra
- the current spectramassTolerance
- the mass error tolerancebubbleScale
- the bubble scale valuefragmentIonLabels
- if true, the fragment ion type is used as the data series key, otherwise the psm index is usedaddMarkers
- if true interval markers for the fragment ions will be shownuseRelativeError
- if true the relative error (ppm) is used instead of the absolute error (Da)
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Method Details
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addFragmentIonTypeMarkers
public static void addFragmentIonTypeMarkers(HashMap<IonMatch,ArrayList<XYZDataPoint>> data, org.jfree.chart.JFreeChart chart, boolean showMarkers)Adds interval markers for all the fragment ion types.- Parameters:
data
- the data to get the interval markers fromchart
- the chart to add the markers toshowMarkers
- if true interval markers for the fragment ions will be added
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getNumberOfDataPointsInPlot
public int getNumberOfDataPointsInPlot()Returns the current number of data points in the mass error plot.- Returns:
- the current number of data points
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addXYZDataSeries
public org.jfree.data.xy.DefaultXYZDataset addXYZDataSeries(HashMap<IonMatch,ArrayList<XYZDataPoint>> data)Adds the provided data series to an XYZ data set.- Parameters:
data
- the data to add- Returns:
- the created data set
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getChartPanel
public org.jfree.chart.ChartPanel getChartPanel()Returns the chart panel.- Returns:
- the chart panel
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