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

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field	Description
static final float	DEFAULT_NON_VISIBLE_MARKER_ALPHA	The default non-visible alpha level.
static final 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

Constructor Summary

Constructors

Constructor	Description
MassErrorBubblePlot()	Empty default constructor
MassErrorBubblePlot(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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

DEFAULT_VISIBLE_MARKER_ALPHA

public static final float DEFAULT_VISIBLE_MARKER_ALPHA

The default visible alpha level.

See Also:

• Constant Field Values

DEFAULT_NON_VISIBLE_MARKER_ALPHA

public static final float DEFAULT_NON_VISIBLE_MARKER_ALPHA

The default non-visible alpha level.

See Also:

• Constant Field Values

Constructor Details

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/labels

annotations - the full list of spectrum annotations

currentSpectra - the current spectra

massTolerance - the mass error tolerance

fragmentIonLabels - if true, the fragment ion type is used as the data series key, otherwise the psm index is used

addMarkers - if true interval markers for the fragment ions will be shown

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/labels

annotations - the full list of spectrum annotations

currentSpectra - the current spectra

massTolerance - the mass error tolerance

fragmentIonLabels - if true, the fragment ion type is used as the data series key, otherwise the psm index is used

addMarkers - if true interval markers for the fragment ions will be shown

useRelativeError - if true the relative error (ppm) is used instead of the absolute error (Da)

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/labels

annotations - the full list of spectrum annotations

currentSpectra - the current spectra

massTolerance - the mass error tolerance

bubbleScale - the bubble scale value

fragmentIonLabels - if true, the fragment ion type is used as the data series key, otherwise the psm index is used

addMarkers - if true interval markers for the fragment ions will be shown

useRelativeError - if true the relative error (ppm) is used instead of the absolute error (Da)

Method Details

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 from

chart - the chart to add the markers to

showMarkers - if true interval markers for the fragment ions will be added

getNumberOfDataPointsInPlot

public int getNumberOfDataPointsInPlot()

Returns the current number of data points in the mass error plot.

Returns:

the current number of data points

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

getChartPanel

public org.jfree.chart.ChartPanel getChartPanel()

Returns the chart panel.

Returns:

the chart panel