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
Constructor Summary |
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot. |
MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
int bubbleScale,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot. |
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 |
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
MassErrorBubblePlot
public MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
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/labelsannotations
- the full list of spectrum annotationscurrentFragmentIons
- the currently selected fragment ion typescurrentSpectra
- the current spectramassTolerance
- the mass error toleranceincludeSinglyCharge
- if singly charged fragment ions are to be includedincludeDoublyCharge
- if doubly charged fragment ions are to be includedincludeMoreThanTwoCharges
- if fragment ions with more than two charges are to be includedfragmentIonLabels
- 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
MassErrorBubblePlot
public MassErrorBubblePlot(ArrayList<String> dataIndexes,
ArrayList<SpectrumAnnotator.SpectrumAnnotationMap> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIons,
ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
int bubbleScale,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
- Creates a new MassErrorBubblePlot.
- Parameters:
dataIndexes
- the data set indexes/labelsannotations
- the full list of spectrum annotationscurrentFragmentIons
- the currently selected fragment ion typescurrentSpectra
- the current spectramassTolerance
- the mass error tolerancebubbleScale
- the bubble scale valueincludeSinglyCharge
- if singly charged fragment ions are to be includedincludeDoublyCharge
- if doubly charged fragment ions are to be includedincludeMoreThanTwoCharges
- if fragment ions with more than two charges are to be includedfragmentIonLabels
- 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
addFragmentIonTypeMarkers
public static void addFragmentIonTypeMarkers(HashMap<String,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
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(HashMap<String,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
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