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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
com.compomics.util.gui.spectrum.MassErrorBubblePlot
public class MassErrorBubblePlot
Creates a MassErrorBubblePlot displaying the mz values vs the mass error with the intensity as the size of the bubbles.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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javax.swing.JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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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 |
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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 |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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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. |
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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. |
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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 | |
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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 |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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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 |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final float DEFAULT_VISIBLE_MARKER_ALPHA
public static final float DEFAULT_NON_VISIBLE_MARKER_ALPHA
Constructor Detail |
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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)
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 shownpublic 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)
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 shownuseRelativeError
- if true the relative error (ppm) is used instead of the absolute error (Da)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)
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 shownuseRelativeError
- if true the relative error (ppm) is used instead of the absolute error (Da)Method Detail |
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public static void addFragmentIonTypeMarkers(java.util.HashMap<java.lang.String,java.util.ArrayList<XYZDataPoint>> data, org.jfree.chart.JFreeChart chart, boolean showMarkers)
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 addedpublic int getNumberOfDataPointsInPlot()
public static org.jfree.data.xy.DefaultXYZDataset addXYZDataSeries(java.util.HashMap<java.lang.String,java.util.ArrayList<XYZDataPoint>> data)
data
- the data to add
public org.jfree.chart.ChartPanel getChartPanel()
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