org.fhcrc.cpl.viewer.quant.gui
Class QuantitationReviewer

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Dialog
                  javax.swing.JDialog
                      org.fhcrc.cpl.viewer.quant.gui.QuantitationReviewer

All Implemented Interfaces:

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

public class QuantitationReviewer
extends javax.swing.JDialog

This is the main GUI screen for Qurate. It uses SwiXML for the menu and for the broad outlines, but most of it is done right here.

See Also:

Serialized Form

Nested Class Summary

protected class	QuantitationReviewer.CreateChartsAction "Create Charts" in the File menu.
class	QuantitationReviewer.EventSummaryTableListSelectionHandler display the properties for the selected event, if only one's selected
protected class	QuantitationReviewer.ExitAction Action to quit
protected class	QuantitationReviewer.FilterPepXMLAction Action to remove bad events and IDs from the file they came from.
static class	QuantitationReviewer.HelpAction Display help from static help file
protected class	QuantitationReviewer.LeftPanelResizeListener Manually manage the size of the properties table
protected class	QuantitationReviewer.OpenFileAction Open a tsv file
protected class	QuantitationReviewer.ProteinSelectedActionListener
protected class	QuantitationReviewer.ProteinSummaryAction
protected class	QuantitationReviewer.RightPanelResizeListener Manually manage the size of the multi-chart panel
protected class	QuantitationReviewer.SaveAction Save changes back to the file we opened TODO: allow saving to different file?
protected class	QuantitationReviewer.SummaryChartsAction Display chart dialog

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

javax.swing.JDialog.AccessibleJDialog

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

java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType

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

protected static org.apache.log4j.Logger	_log
javax.swing.Action	aboutAction
protected javax.swing.JTextField	assessmentDescTextField
javax.swing.JPanel	assessmentPanel
protected javax.swing.JTextField	assessmentTypeTextField
protected int	chartPaneHeight
protected javax.swing.JTextField	commentTextField
javax.swing.JPanel	contentPanel
javax.swing.Action	createChartsAction
javax.swing.JPanel	curationPanel
protected int	displayedEventIndex
protected java.awt.Frame	eventSummaryFrame
protected QuantEventsSummaryTable	eventSummaryTable
javax.swing.Action	exitAction
javax.swing.Action	filterPepXMLAction
protected javax.swing.JButton	filterPepXMLButton
protected int	fullHeight
protected int	fullWidth
javax.swing.Action	helpAction
protected javax.swing.ButtonGroup	idCurationButtonGroup
protected int	imagePanelWidth
javax.swing.JPanel	leftPanel
protected int	leftPanelWidth
javax.swing.JLabel	messageLabel
protected TabbedMultiChartDisplayPanel	multiChartDisplay
javax.swing.JPanel	navigationPanel
protected javax.swing.JRadioButton	onePeakRatioRadioButton
javax.swing.Action	openFileAction
protected int	propertiesHeight
protected javax.swing.JScrollPane	propertiesScrollPane
protected QuantEvent.QuantEventPropertiesTable	propertiesTable
protected int	propertiesWidth
javax.swing.Action	proteinSummaryAction
protected ProteinSummarySelectorFrame	proteinSummarySelector
protected javax.swing.ButtonGroup	quantCurationButtonGroup
protected java.io.File	quantFile
protected ProteinQuantSummaryFrame	quantSummaryFrame
javax.swing.JPanel	rightPanel
protected int	rightPanelWidth
javax.swing.Action	saveAction
protected javax.swing.JButton	saveChangesButton
ProteinQuantChartsCLM	settingsCLM
protected SplashFrame	splashFrame
protected java.net.URL	splashImageURL
javax.swing.JSplitPane	splitPane
javax.swing.JPanel	statusPanel
javax.swing.Action	summaryChartsAction
protected javax.swing.JFrame	summaryChartsFrame
protected TabbedMultiChartDisplayPanel	summaryChartsPanel
protected PanelWithPeakChart	theoreticalPeaksChart
javax.swing.JPanel	theoreticalPeaksPanel
protected int	theoreticalPeaksPanelHeight

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

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, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

QuantitationReviewer()
No-arg constructor doesn't pop up a file chooser, but it does show splash screen

QuantitationReviewer(boolean showSplash, boolean showFileOpen)

QuantitationReviewer(java.io.File quantFile)

QuantitationReviewer(java.util.List<QuantEvent> quantEvents)

Method Summary

protected void	buildSummaryCharts() Build summary charts for all displayed events.
void	buttonBack_actionPerformed(java.awt.event.ActionEvent event)
void	buttonCuration_actionPerformed(java.awt.event.ActionEvent event)
void	buttonForward_actionPerformed(java.awt.event.ActionEvent event)
void	buttonIDCuration_actionPerformed(java.awt.event.ActionEvent event)
void	buttonShowEventSummary_actionPerformed(java.awt.event.ActionEvent event)
protected void	displayCurrentQuantEvent(boolean shouldUpdateTable) Take care of the charts and the properties panel
void	displayQuantEvents(java.util.List<QuantEvent> quantEvents)
void	displayQuantFile(java.io.File quantFile)
void	dispose() Clean up the windows that might be open
protected void	errorMessage(java.lang.String message, java.lang.Throwable t) Display a dialog box with info message and stack trace
static void	filterBadEventsFromFile(java.util.List<QuantEvent> quantEvents, java.io.File pepXmlFile, java.io.File outFile) Remove all the events the user has designated as 'bad' from the pepXML file they came from TODO: report how many events weren't found
int	getDisplayedEventIndex()
java.io.File	getQuantFile()
static void	infoMessage(java.lang.String message) Display a dialog box with info message
protected void	initGUI() Initialize all GUI components and display the UI
void	setDisplayedEventIndex(int displayedEventIndex)
void	setMessage(java.lang.String message) Set status message.
void	setQuantFile(java.io.File quantFile)
void	showProteinQuantSummaryFrame(java.util.List<ProtXmlReader.Protein> proteins)
void	showProteinQuantSummaryFrame(java.util.List<ProtXmlReader.Protein> proteins, java.util.Map<java.lang.String,java.util.List<java.lang.String>> proteinGenesMap)
protected void	showSplashScreen() Displays the splash screen.
protected void	showTheoreticalPeaks() Calculate and show theoretical isotopic distribution peaks, with light encroaching on heavy if necessary
protected void	updateUIAfterChange(boolean shouldUpdateTable) Update lots of UI components after a change of quantitation event

Methods inherited from class javax.swing.JDialog

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

Methods inherited from class java.awt.Dialog

addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setModal, setModalityType, setResizable, setTitle, setUndecorated, setVisible, show, toBack

Methods inherited from class java.awt.Window

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

Field Detail

quantFile

protected java.io.File quantFile

multiChartDisplay

protected TabbedMultiChartDisplayPanel multiChartDisplay

displayedEventIndex

protected int displayedEventIndex

contentPanel

public javax.swing.JPanel contentPanel

splitPane

public javax.swing.JSplitPane splitPane

leftPanel

public javax.swing.JPanel leftPanel

rightPanel

public javax.swing.JPanel rightPanel

navigationPanel

public javax.swing.JPanel navigationPanel

settingsCLM

public ProteinQuantChartsCLM settingsCLM

splashFrame

protected SplashFrame splashFrame

splashImageURL

protected final java.net.URL splashImageURL

curationPanel

public javax.swing.JPanel curationPanel

quantCurationButtonGroup

protected javax.swing.ButtonGroup quantCurationButtonGroup

onePeakRatioRadioButton

protected javax.swing.JRadioButton onePeakRatioRadioButton

idCurationButtonGroup

protected javax.swing.ButtonGroup idCurationButtonGroup

saveChangesButton

protected javax.swing.JButton saveChangesButton

filterPepXMLButton

protected javax.swing.JButton filterPepXMLButton

commentTextField

protected javax.swing.JTextField commentTextField

assessmentPanel

public javax.swing.JPanel assessmentPanel

assessmentTypeTextField

protected javax.swing.JTextField assessmentTypeTextField

assessmentDescTextField

protected javax.swing.JTextField assessmentDescTextField

quantSummaryFrame

protected ProteinQuantSummaryFrame quantSummaryFrame

theoreticalPeaksPanel

public javax.swing.JPanel theoreticalPeaksPanel

theoreticalPeaksChart

protected PanelWithPeakChart theoreticalPeaksChart

proteinSummarySelector

protected ProteinSummarySelectorFrame proteinSummarySelector

helpAction

public javax.swing.Action helpAction

exitAction

public javax.swing.Action exitAction

openFileAction

public javax.swing.Action openFileAction

createChartsAction

public javax.swing.Action createChartsAction

saveAction

public javax.swing.Action saveAction

filterPepXMLAction

public javax.swing.Action filterPepXMLAction

proteinSummaryAction

public javax.swing.Action proteinSummaryAction

aboutAction

public javax.swing.Action aboutAction

summaryChartsAction

public javax.swing.Action summaryChartsAction

eventSummaryTable

protected QuantEventsSummaryTable eventSummaryTable

eventSummaryFrame

protected java.awt.Frame eventSummaryFrame

propertiesTable

protected QuantEvent.QuantEventPropertiesTable propertiesTable

propertiesScrollPane

protected javax.swing.JScrollPane propertiesScrollPane

statusPanel

public javax.swing.JPanel statusPanel

messageLabel

public javax.swing.JLabel messageLabel

leftPanelWidth

protected int leftPanelWidth

rightPanelWidth

protected int rightPanelWidth

imagePanelWidth

protected int imagePanelWidth

fullWidth

protected int fullWidth

fullHeight

protected int fullHeight

propertiesWidth

protected int propertiesWidth

propertiesHeight

protected int propertiesHeight

chartPaneHeight

protected int chartPaneHeight

theoreticalPeaksPanelHeight

protected int theoreticalPeaksPanelHeight

summaryChartsFrame

protected javax.swing.JFrame summaryChartsFrame

summaryChartsPanel

protected TabbedMultiChartDisplayPanel summaryChartsPanel

_log

protected static org.apache.log4j.Logger _log

Constructor Detail

QuantitationReviewer

public QuantitationReviewer(boolean showSplash,
                            boolean showFileOpen)

QuantitationReviewer

public QuantitationReviewer()

No-arg constructor doesn't pop up a file chooser, but it does show splash screen

QuantitationReviewer

public QuantitationReviewer(java.util.List<QuantEvent> quantEvents)

QuantitationReviewer

public QuantitationReviewer(java.io.File quantFile)
                     throws java.io.IOException

Throws:

java.io.IOException

Method Detail

displayQuantEvents

public void displayQuantEvents(java.util.List<QuantEvent> quantEvents)

displayQuantFile

public void displayQuantFile(java.io.File quantFile)
                      throws java.io.IOException

Throws:

java.io.IOException

initGUI

protected void initGUI()

Initialize all GUI components and display the UI

buttonBack_actionPerformed

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

buttonForward_actionPerformed

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

buttonShowEventSummary_actionPerformed

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

buttonCuration_actionPerformed

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

buttonIDCuration_actionPerformed

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

buildSummaryCharts

protected void buildSummaryCharts()

Build summary charts for all displayed events. At the moment, there's just one chart, a scatterplot of algorithm vs singlepeak ratio (log) that's clickable to navigate between events

updateUIAfterChange

protected void updateUIAfterChange(boolean shouldUpdateTable)

Update lots of UI components after a change of quantitation event

showTheoreticalPeaks

protected void showTheoreticalPeaks()

Calculate and show theoretical isotopic distribution peaks, with light encroaching on heavy if necessary

displayCurrentQuantEvent

protected void displayCurrentQuantEvent(boolean shouldUpdateTable)

Take care of the charts and the properties panel

Parameters:

shouldUpdateTable - Should we update the events table? Need this to avoid infinite loop

getDisplayedEventIndex

public int getDisplayedEventIndex()

setDisplayedEventIndex

public void setDisplayedEventIndex(int displayedEventIndex)

infoMessage

public static void infoMessage(java.lang.String message)

Display a dialog box with info message

Parameters:

message -

errorMessage

protected void errorMessage(java.lang.String message,
                            java.lang.Throwable t)

Display a dialog box with info message and stack trace

Parameters:

message -

t -

filterBadEventsFromFile

public static void filterBadEventsFromFile(java.util.List<QuantEvent> quantEvents,
                                           java.io.File pepXmlFile,
                                           java.io.File outFile)
                                    throws java.io.IOException,
                                           javax.xml.stream.XMLStreamException

Remove all the events the user has designated as 'bad' from the pepXML file they came from TODO: report how many events weren't found

Parameters:

quantEvents -

pepXmlFile -

outFile -

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

setMessage

public void setMessage(java.lang.String message)

Set status message. Separate thread necessary or UI hangs

Parameters:

message -

showProteinQuantSummaryFrame

public void showProteinQuantSummaryFrame(java.util.List<ProtXmlReader.Protein> proteins)

showProteinQuantSummaryFrame

public void showProteinQuantSummaryFrame(java.util.List<ProtXmlReader.Protein> proteins,
                                         java.util.Map<java.lang.String,java.util.List<java.lang.String>> proteinGenesMap)

dispose

public void dispose()

Clean up the windows that might be open

Overrides:

dispose in class java.awt.Window

getQuantFile

public java.io.File getQuantFile()

setQuantFile

public void setQuantFile(java.io.File quantFile)

showSplashScreen

protected void showSplashScreen()

Displays the splash screen. Side effect: sets the splashFrame variable, so it can be disposed later