com.compomics.util.gui.spectrum
Class MassErrorBubblePlot

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by com.compomics.util.gui.spectrum.MassErrorBubblePlot
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class MassErrorBubblePlot
extends javax.swing.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
javax.swing.JPanel.AccessibleJPanel
 
Nested classes/interfaces inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
Nested classes/interfaces inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
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
accessibleContext, 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
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
MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes, java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations, java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, java.util.ArrayList<MSnSpectrum> currentSpectra, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers)
          Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes, java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations, java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, java.util.ArrayList<MSnSpectrum> currentSpectra, double massTolerance, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
          Creates a new MassErrorBubblePlot.
MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes, java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations, java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons, java.util.ArrayList<MSnSpectrum> currentSpectra, double massTolerance, double bubbleScale, boolean includeSinglyCharge, boolean includeDoublyCharge, boolean includeMoreThanTwoCharges, boolean fragmentIonLabels, boolean addMarkers, boolean useRelativeError)
          Creates a new MassErrorBubblePlot.
 
Method Summary
static void addFragmentIonTypeMarkers(java.util.HashMap<java.lang.String,java.util.ArrayList<XYZDataPoint>> data, org.jfree.chart.JFreeChart chart, boolean showMarkers)
          Adds interval markers for all the fragment ion types.
static org.jfree.data.xy.DefaultXYZDataset addXYZDataSeries(java.util.HashMap<java.lang.String,java.util.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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, 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, transferFocusBackward, 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, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, 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, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

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 Detail

MassErrorBubblePlot

public MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
                           java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
                           java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
                           java.util.ArrayList<MSnSpectrum> currentSpectra,
                           double massTolerance,
                           boolean includeSinglyCharge,
                           boolean includeDoublyCharge,
                           boolean includeMoreThanTwoCharges,
                           boolean fragmentIonLabels,
                           boolean addMarkers)
Creates a new MassErrorBubblePlot.

Parameters:
dataIndexes - the data set indexes/labels
annotations - the full list of spectrum annotations
currentFragmentIons - the currently selected fragment ion types
currentSpectra - the current spectra
massTolerance - the mass error tolerance
includeSinglyCharge - if singly charged fragment ions are to be included
includeDoublyCharge - if doubly charged fragment ions are to be included
includeMoreThanTwoCharges - if fragment ions with more than two charges are to be included
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(java.util.ArrayList<java.lang.String> dataIndexes,
                           java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
                           java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
                           java.util.ArrayList<MSnSpectrum> currentSpectra,
                           double massTolerance,
                           boolean includeSinglyCharge,
                           boolean includeDoublyCharge,
                           boolean includeMoreThanTwoCharges,
                           boolean fragmentIonLabels,
                           boolean addMarkers,
                           boolean useRelativeError)
Creates a new MassErrorBubblePlot.

Parameters:
dataIndexes - the data set indexes/labels
annotations - the full list of spectrum annotations
currentFragmentIons - the currently selected fragment ion types
currentSpectra - the current spectra
massTolerance - the mass error tolerance
includeSinglyCharge - if singly charged fragment ions are to be included
includeDoublyCharge - if doubly charged fragment ions are to be included
includeMoreThanTwoCharges - if fragment ions with more than two charges are to be included
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(java.util.ArrayList<java.lang.String> dataIndexes,
                           java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
                           java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
                           java.util.ArrayList<MSnSpectrum> currentSpectra,
                           double massTolerance,
                           double bubbleScale,
                           boolean includeSinglyCharge,
                           boolean includeDoublyCharge,
                           boolean includeMoreThanTwoCharges,
                           boolean fragmentIonLabels,
                           boolean addMarkers,
                           boolean useRelativeError)
Creates a new MassErrorBubblePlot.

Parameters:
dataIndexes - the data set indexes/labels
annotations - the full list of spectrum annotations
currentFragmentIons - the currently selected fragment ion types
currentSpectra - the current spectra
massTolerance - the mass error tolerance
bubbleScale - the bubble scale value
includeSinglyCharge - if singly charged fragment ions are to be included
includeDoublyCharge - if doubly charged fragment ions are to be included
includeMoreThanTwoCharges - if fragment ions with more than two charges are to be included
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 Detail

addFragmentIonTypeMarkers

public static void addFragmentIonTypeMarkers(java.util.HashMap<java.lang.String,java.util.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 static org.jfree.data.xy.DefaultXYZDataset addXYZDataSeries(java.util.HashMap<java.lang.String,java.util.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


Copyright © 2012. All Rights Reserved.