org.fhcrc.cpl.viewer.gui
Class MRMDialog

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      org.fhcrc.cpl.viewer.gui.MRMDialog

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class MRMDialog
extends javax.swing.JFrame
implements java.io.Serializable

GUI

See Also:

Serialized Form

Nested Class Summary

class	MRMDialog.coloredMRMListRenderer
class	MRMDialog.daughterRangeAxisChangeListener
class	MRMDialog.defaultGraphZone
class	MRMDialog.domainAxisZoomCoordinator
class	MRMDialog.MRMTransitionTableRenderer
static interface	MRMDialog.mzXML2TransitionArray
protected class	MRMDialog.originalReParser
static class	MRMDialog.peaksData
class	MRMDialog.peaksTableListener
class	MRMDialog.PeaksTableListSelectionListener
class	MRMDialog.peaksTableSelectionModel
protected class	MRMDialog.thermoReParser
class	MRMDialog.transitionListSelectionListener
class	MRMDialog.zoomedGraphZone
class	MRMDialog.zoomToCurveGraphZone

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

javax.swing.JFrame.AccessibleJFrame

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

java.awt.Frame.AccessibleAWTFrame

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

java.awt.Window.AccessibleAWTWindow

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

boolean	_conn
protected float	_daughterMzTolerance
java.lang.Class	_ecurveclass
protected javax.swing.JFileChooser	_imageOutputFileChooser
protected javax.swing.JFileChooser	_inputTSVFileChooser
float	_minAreaCutoff
float	_minPeakCutoff
protected MRMTransition[]	_mrmTransitions
protected java.io.File	_mzXMLFile
protected javax.swing.JFileChooser	_mzXMLFileChooser
protected javax.swing.JFileChooser	_outputFileChooser
protected float	_precursorChromatogramWindow
protected float	_precursorDiscoveryMzTolerance
protected javax.swing.event.ListSelectionListener	_ptmlsl
protected MSRun	_run
float	_sictol
boolean	_sim
protected boolean	_synclh
protected MRMDialog.transitionListSelectionListener	_tlsl
protected boolean	_traceAllFragments
javax.swing.JButton	buttonAccept
javax.swing.JButton	buttonBoost
javax.swing.JButton	buttonFindMate
javax.swing.JButton	buttonNext
javax.swing.JButton	buttonPrev
javax.swing.JButton	buttonReject
javax.swing.JButton	buttonRejectGroup
javax.swing.JButton	buttonSave
javax.swing.JButton	buttonTiming
javax.swing.JButton	buttonZC
javax.swing.JButton	buttonZoom
java.awt.Container	contentPanel
protected int	currentTransitionIndex
javax.swing.JPanel	daughterContainerContainerPanel
javax.swing.JPanel	daughterContainerPanel
protected javax.swing.JLabel	elutionTableLabel
javax.swing.JLabel	fileNameLabel
javax.swing.JScrollPane	listScrollPane
javax.swing.JList	listTransition
javax.swing.JMenuBar	menuBarMain
javax.swing.JMenu	menuFile
javax.swing.JMenu	menuHelp
javax.swing.JMenuItem	menuItemAMin
javax.swing.JMenuItem	menuItemArguments
javax.swing.JMenuItem	menuItemChangeStrategy
javax.swing.JMenuItem	menuItemDaughterDiscTol
javax.swing.JMenuItem	menuItemDefinitions
javax.swing.JMenuItem	menuItemLoadTSV
javax.swing.JMenuItem	menuItemOpen
javax.swing.JMenuItem	menuItemOptions
javax.swing.JMenuItem	menuItemPMin
javax.swing.JMenuItem	menuItemPrecDiscTol
javax.swing.JMenuItem	menuItemQuit
javax.swing.JMenuItem	menuItemSaveImage
javax.swing.JMenuItem	menuItemSICtolerance
javax.swing.JMenuItem	menuItemSyncLH
javax.swing.JMenuItem	menuItemTips
javax.swing.JMenuItem	menuItemTraceAllFragments
javax.swing.JMenu	menuOptions
org.jfree.chart.plot.XYPlot	oldPrecursorChart
org.jfree.chart.plot.XYPlot	oldProductChart
javax.swing.JScrollPane	peaksScrollPane
static javax.swing.JTable	peaksTable
javax.swing.JPanel	precursorContainerContainerPanel
javax.swing.JPanel	precursorContainerPanel
protected javax.swing.JLabel	titleText
javax.swing.JLabel	topGraphLabel
TransitionDefinitionHeader	transDefHeader
MRMTransition	transitionOnPlot

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

MRMDialog(java.io.File mzXMLFile, float precDiscTol, float daughterTol, float chromTol, java.lang.Class ECurveStrat, boolean traceAllFragments, boolean synclh, float minP, float minA)
Initialize the GUI and show the first transition

Method Summary

void	AQUAinitializations()
void	buttonAccept_actionPerformed(java.awt.event.ActionEvent event)
void	buttonBoost_actionPerformed(java.awt.event.ActionEvent event)
void	buttonDTOL_actionPerformed(java.awt.event.ActionEvent event)
void	buttonFindMate_actionPerformed(java.awt.event.ActionEvent event)
void	buttonNext_actionPerformed(java.awt.event.ActionEvent event)
void	buttonPDT_actionPerformed(java.awt.event.ActionEvent event)
void	buttonPostPressTasks()
void	buttonPrev_actionPerformed(java.awt.event.ActionEvent event)
void	buttonReject_actionPerformed(java.awt.event.ActionEvent event)
void	buttonRejectGroup_actionPerformed(java.awt.event.ActionEvent event)
void	buttonSave_actionPerformed(java.awt.event.ActionEvent event)
void	buttonSICUpdate_actionPerformed(java.awt.event.ActionEvent event)
void	buttonTiming_actionPerformed(java.awt.event.ActionEvent event)
void	buttonZC_actionPerformed(java.awt.event.ActionEvent event)
void	buttonZoom_actionPerformed(java.awt.event.ActionEvent event)
protected void	clearPreviousChartJunk(org.jfree.chart.plot.XYPlot xyp)
void	contentPanel_componentResized(java.awt.event.ComponentEvent event)
void	contentPanel_mouseClicked(java.awt.event.MouseEvent event)
protected void	createChartInPanel(javax.swing.JPanel parentPanel, org.jfree.data.xy.XYSeriesCollection dataset, java.lang.Double domainMin, java.lang.Double domainMax, org.jfree.chart.plot.DrawingSupplier supplier, org.fhcrc.cpl.viewer.gui.MRMDialog.whichGraph wg) Draw a chart in a panel.
protected void	createChartInPanelDaughterTasksOnly(org.jfree.chart.plot.XYPlot xyp)
protected void	createChartInPanelPrecursorTasksOnly(org.jfree.chart.plot.XYPlot xyp)
protected org.jfree.chart.plot.DrawingSupplier	getDrawingSupplierForPlot(MRMTransition plot)
protected double	getMaxRetentionTimeForPlot(MRMTransition plot)
protected double	getMinRetentionTimeForPlot(MRMTransition plot)
void	initStuff()
protected org.jfree.data.xy.XYSeries	makeParentSeries(MRMTransition parent)
void	menuItemAMin_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemArguments_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemChangeStrategy_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemDefinitions_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemLoadTSV_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemOpen_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemOptions_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemPMin_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemQuit_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemSaveImage_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemSyncLH_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemTips_actionPerformed(java.awt.event.ActionEvent event)
void	menuItemTraceAllFragments_actionPerformed(java.awt.event.ActionEvent event)
boolean	precursorChromatogramEmpty(MRMTransition parent)
protected void	scrollPeakTableToRow(int row)
protected void	scrollPeakTableToTransition(MRMTransition trans)
void	updateChartsAndFields(boolean clear)
void	updateChartsAndFields(graphZone gz)
protected void	updateDaughterCharts(boolean clear)
protected void	updateDaughterCharts(boolean clear, graphZone gz)
protected void	updateDaughterCharts(graphZone gz)
protected void	updatePrecursorChart(boolean clear)
protected void	updatePrecursorChart(boolean clear, graphZone gz)
protected void	updatePrecursorChart(graphZone gz)

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOwnedWindows, getOwner, getOwnerlessWindows, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setVisible, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

titleText

protected javax.swing.JLabel titleText

elutionTableLabel

protected javax.swing.JLabel elutionTableLabel

_mrmTransitions

protected MRMTransition[] _mrmTransitions

currentTransitionIndex

protected int currentTransitionIndex

_run

protected MSRun _run

_precursorDiscoveryMzTolerance

protected float _precursorDiscoveryMzTolerance

_daughterMzTolerance

protected float _daughterMzTolerance

_precursorChromatogramWindow

protected float _precursorChromatogramWindow

_mzXMLFile

protected java.io.File _mzXMLFile

_mzXMLFileChooser

protected javax.swing.JFileChooser _mzXMLFileChooser

_outputFileChooser

protected javax.swing.JFileChooser _outputFileChooser

_inputTSVFileChooser

protected javax.swing.JFileChooser _inputTSVFileChooser

_imageOutputFileChooser

protected javax.swing.JFileChooser _imageOutputFileChooser

_traceAllFragments

protected boolean _traceAllFragments

_ptmlsl

protected javax.swing.event.ListSelectionListener _ptmlsl

_tlsl

protected MRMDialog.transitionListSelectionListener _tlsl

_synclh

protected boolean _synclh

listTransition

public javax.swing.JList listTransition

listScrollPane

public javax.swing.JScrollPane listScrollPane

peaksScrollPane

public javax.swing.JScrollPane peaksScrollPane

peaksTable

public static javax.swing.JTable peaksTable

fileNameLabel

public javax.swing.JLabel fileNameLabel

precursorContainerPanel

public javax.swing.JPanel precursorContainerPanel

precursorContainerContainerPanel

public javax.swing.JPanel precursorContainerContainerPanel

daughterContainerContainerPanel

public javax.swing.JPanel daughterContainerContainerPanel

daughterContainerPanel

public javax.swing.JPanel daughterContainerPanel

topGraphLabel

public javax.swing.JLabel topGraphLabel

buttonZC

public javax.swing.JButton buttonZC

buttonPrev

public javax.swing.JButton buttonPrev

buttonNext

public javax.swing.JButton buttonNext

buttonSave

public javax.swing.JButton buttonSave

buttonAccept

public javax.swing.JButton buttonAccept

buttonReject

public javax.swing.JButton buttonReject

buttonZoom

public javax.swing.JButton buttonZoom

buttonFindMate

public javax.swing.JButton buttonFindMate

buttonBoost

public javax.swing.JButton buttonBoost

buttonTiming

public javax.swing.JButton buttonTiming

buttonRejectGroup

public javax.swing.JButton buttonRejectGroup

menuBarMain

public javax.swing.JMenuBar menuBarMain

menuFile

public javax.swing.JMenu menuFile

menuItemQuit

public javax.swing.JMenuItem menuItemQuit

menuItemOpen

public javax.swing.JMenuItem menuItemOpen

menuItemLoadTSV

public javax.swing.JMenuItem menuItemLoadTSV

menuOptions

public javax.swing.JMenu menuOptions

menuHelp

public javax.swing.JMenu menuHelp

menuItemArguments

public javax.swing.JMenuItem menuItemArguments

menuItemOptions

public javax.swing.JMenuItem menuItemOptions

menuItemDefinitions

public javax.swing.JMenuItem menuItemDefinitions

menuItemTips

public javax.swing.JMenuItem menuItemTips

menuItemSICtolerance

public javax.swing.JMenuItem menuItemSICtolerance

menuItemPrecDiscTol

public javax.swing.JMenuItem menuItemPrecDiscTol

menuItemDaughterDiscTol

public javax.swing.JMenuItem menuItemDaughterDiscTol

menuItemTraceAllFragments

public javax.swing.JMenuItem menuItemTraceAllFragments

menuItemChangeStrategy

public javax.swing.JMenuItem menuItemChangeStrategy

menuItemSyncLH

public javax.swing.JMenuItem menuItemSyncLH

menuItemPMin

public javax.swing.JMenuItem menuItemPMin

menuItemAMin

public javax.swing.JMenuItem menuItemAMin

menuItemSaveImage

public javax.swing.JMenuItem menuItemSaveImage

_sim

public boolean _sim

_conn

public boolean _conn

_sictol

public float _sictol

_ecurveclass

public java.lang.Class _ecurveclass

contentPanel

public java.awt.Container contentPanel

transitionOnPlot

public MRMTransition transitionOnPlot

transDefHeader

public TransitionDefinitionHeader transDefHeader

_minPeakCutoff

public float _minPeakCutoff

_minAreaCutoff

public float _minAreaCutoff

oldPrecursorChart

public org.jfree.chart.plot.XYPlot oldPrecursorChart

oldProductChart

public org.jfree.chart.plot.XYPlot oldProductChart

Constructor Detail

MRMDialog

public MRMDialog(java.io.File mzXMLFile,
                 float precDiscTol,
                 float daughterTol,
                 float chromTol,
                 java.lang.Class ECurveStrat,
                 boolean traceAllFragments,
                 boolean synclh,
                 float minP,
                 float minA)

Initialize the GUI and show the first transition

Parameters:

mzXMLFile -

Method Detail

AQUAinitializations

public void AQUAinitializations()

initStuff

public void initStuff()

buttonPostPressTasks

public void buttonPostPressTasks()

buttonSICUpdate_actionPerformed

public void buttonSICUpdate_actionPerformed(java.awt.event.ActionEvent event)

buttonPDT_actionPerformed

public void buttonPDT_actionPerformed(java.awt.event.ActionEvent event)

buttonDTOL_actionPerformed

public void buttonDTOL_actionPerformed(java.awt.event.ActionEvent event)

menuItemPMin_actionPerformed

public void menuItemPMin_actionPerformed(java.awt.event.ActionEvent event)

menuItemAMin_actionPerformed

public void menuItemAMin_actionPerformed(java.awt.event.ActionEvent event)

menuItemQuit_actionPerformed

public void menuItemQuit_actionPerformed(java.awt.event.ActionEvent event)

menuItemTraceAllFragments_actionPerformed

public void menuItemTraceAllFragments_actionPerformed(java.awt.event.ActionEvent event)

menuItemSyncLH_actionPerformed

public void menuItemSyncLH_actionPerformed(java.awt.event.ActionEvent event)

menuItemChangeStrategy_actionPerformed

public void menuItemChangeStrategy_actionPerformed(java.awt.event.ActionEvent event)

menuItemOpen_actionPerformed

public void menuItemOpen_actionPerformed(java.awt.event.ActionEvent event)

menuItemLoadTSV_actionPerformed

public void menuItemLoadTSV_actionPerformed(java.awt.event.ActionEvent event)

menuItemTips_actionPerformed

public void menuItemTips_actionPerformed(java.awt.event.ActionEvent event)

menuItemDefinitions_actionPerformed

public void menuItemDefinitions_actionPerformed(java.awt.event.ActionEvent event)

menuItemOptions_actionPerformed

public void menuItemOptions_actionPerformed(java.awt.event.ActionEvent event)

menuItemArguments_actionPerformed

public void menuItemArguments_actionPerformed(java.awt.event.ActionEvent event)

buttonSave_actionPerformed

public void buttonSave_actionPerformed(java.awt.event.ActionEvent event)

menuItemSaveImage_actionPerformed

public void menuItemSaveImage_actionPerformed(java.awt.event.ActionEvent event)

buttonZC_actionPerformed

public void buttonZC_actionPerformed(java.awt.event.ActionEvent event)

buttonZoom_actionPerformed

public void buttonZoom_actionPerformed(java.awt.event.ActionEvent event)

buttonNext_actionPerformed

public void buttonNext_actionPerformed(java.awt.event.ActionEvent event)

buttonPrev_actionPerformed

public void buttonPrev_actionPerformed(java.awt.event.ActionEvent event)

buttonReject_actionPerformed

public void buttonReject_actionPerformed(java.awt.event.ActionEvent event)

buttonRejectGroup_actionPerformed

public void buttonRejectGroup_actionPerformed(java.awt.event.ActionEvent event)

buttonAccept_actionPerformed

public void buttonAccept_actionPerformed(java.awt.event.ActionEvent event)

buttonBoost_actionPerformed

public void buttonBoost_actionPerformed(java.awt.event.ActionEvent event)

buttonTiming_actionPerformed

public void buttonTiming_actionPerformed(java.awt.event.ActionEvent event)

buttonFindMate_actionPerformed

public void buttonFindMate_actionPerformed(java.awt.event.ActionEvent event)

contentPanel_componentResized

public void contentPanel_componentResized(java.awt.event.ComponentEvent event)

contentPanel_mouseClicked

public void contentPanel_mouseClicked(java.awt.event.MouseEvent event)

getDrawingSupplierForPlot

protected org.jfree.chart.plot.DrawingSupplier getDrawingSupplierForPlot(MRMTransition plot)

scrollPeakTableToRow

protected void scrollPeakTableToRow(int row)

scrollPeakTableToTransition

protected void scrollPeakTableToTransition(MRMTransition trans)

updateDaughterCharts

protected void updateDaughterCharts(boolean clear,
                                    graphZone gz)

updateDaughterCharts

protected void updateDaughterCharts(boolean clear)

updateDaughterCharts

protected void updateDaughterCharts(graphZone gz)

updatePrecursorChart

protected void updatePrecursorChart(boolean clear,
                                    graphZone gz)

updatePrecursorChart

protected void updatePrecursorChart(boolean clear)

updatePrecursorChart

protected void updatePrecursorChart(graphZone gz)

updateChartsAndFields

public void updateChartsAndFields(boolean clear)

updateChartsAndFields

public void updateChartsAndFields(graphZone gz)

getMinRetentionTimeForPlot

protected double getMinRetentionTimeForPlot(MRMTransition plot)

getMaxRetentionTimeForPlot

protected double getMaxRetentionTimeForPlot(MRMTransition plot)

makeParentSeries

protected org.jfree.data.xy.XYSeries makeParentSeries(MRMTransition parent)

precursorChromatogramEmpty

public boolean precursorChromatogramEmpty(MRMTransition parent)

createChartInPanelPrecursorTasksOnly

protected void createChartInPanelPrecursorTasksOnly(org.jfree.chart.plot.XYPlot xyp)

createChartInPanelDaughterTasksOnly

protected void createChartInPanelDaughterTasksOnly(org.jfree.chart.plot.XYPlot xyp)

clearPreviousChartJunk

protected void clearPreviousChartJunk(org.jfree.chart.plot.XYPlot xyp)

createChartInPanel

protected void createChartInPanel(javax.swing.JPanel parentPanel,
                                  org.jfree.data.xy.XYSeriesCollection dataset,
                                  java.lang.Double domainMin,
                                  java.lang.Double domainMax,
                                  org.jfree.chart.plot.DrawingSupplier supplier,
                                  org.fhcrc.cpl.viewer.gui.MRMDialog.whichGraph wg)

Draw a chart in a panel. Good for precursors and daughters

Parameters:

parentPanel -

dataset -

domainMin -

domainMax -

supplier -

wg -