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

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

All Implemented Interfaces:

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

public class ProteinSummarySelectorFrame
extends javax.swing.JFrame

A window displaying a table with info on all the quantitated proteins in a protXML file. A single row, or multiple may be selected and the quantitative events pulled up in a ProteinQuantSummaryFrame. Gene information for proteins can optionally be pulled from a protein-gene mapping file, in which case the Gene column of the table will be populated. The table is sortable on all columns

See Also:

Serialized Form

Nested Class Summary

protected class	ProteinSummarySelectorFrame.LogRatioHistogramListener A chart listener that picks up events indicating changes to the selected area
static class	ProteinSummarySelectorFrame.ProteinRatioAscComparator Sort proteins by ratio, ascending
static class	ProteinSummarySelectorFrame.ProteinSummaryTable Sortable on all columns

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

protected static org.apache.log4j.Logger	_log
protected boolean	allowMultipleSelection
protected javax.swing.JButton	buttonDeselectAll
protected javax.swing.JButton	buttonSaveTSV
protected javax.swing.JButton	buttonSelectAllVisible
protected javax.swing.JButton	buttonSelectedProtein
protected javax.swing.JButton	buttonShowEvents
javax.swing.JPanel	contentPanel
protected int	height
protected int	LOGRATIO_HISTOGRAM_PANEL_HEIGHT
PanelWithLogRatioHistAndFields	logRatioHistogramPanel
javax.swing.JPanel	mainPanel
protected float	maxLowRatio
javax.swing.JLabel	maxLowRatioLabel
javax.swing.JLabel	messageLabel
protected float	minHighRatio
javax.swing.JLabel	minHighRatioLabel
protected float	minProteinProphet
javax.swing.JLabel	numPassingProteinsLabel
protected java.util.Map<java.lang.String,java.util.List<java.lang.String>>	proteinGeneMap
protected java.util.Map<ProtXmlReader.Protein,java.lang.Integer>	proteinGroupNumberMap
protected java.util.List<ProtXmlReader.Protein>	proteins
protected ProteinSummarySelectorFrame.ProteinSummaryTable	proteinSummaryTable
protected java.util.List<ProtXmlReader.Protein>	selectedProteins
javax.swing.JPanel	statusPanel
protected int	STATUSPANEL_HEIGHT
javax.swing.JPanel	summaryPanel
protected int	SUMMARYPANEL_HEIGHT
protected int	TABLEROW_HEIGHT
protected javax.swing.ListSelectionModel	tableSelectionModel
protected int	TITLEBAR_HEIGHT
protected int	width

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

ProteinSummarySelectorFrame()

ProteinSummarySelectorFrame(boolean allowMultipleSelection)

ProteinSummarySelectorFrame(java.io.File protXmlFile)

Method Summary

void	addSelectionListener(java.awt.event.ActionListener listener) Add a listener for selecting a row in the table.
void	buttonCancel_actionPerformed(java.awt.event.ActionEvent event) Quit
void	buttonDeselectAll_actionPerformed(java.awt.event.ActionEvent event) Deselect all currently-selected rows, whether or not they're currently passing the filter
void	buttonSaveTSV_actionPerformed(java.awt.event.ActionEvent event) Save the table contents as a TSV file
void	buttonSelectAllVisible_actionPerformed(java.awt.event.ActionEvent event) Select all currently-visible (i.e., passes filter) rows
void	buttonShowEvents_actionPerformed(java.awt.event.ActionEvent event) Show the detail screen with a table of the actual events for this/these protein(s)
void	displayProteins()
void	displayProteins(java.io.File protXmlFile) Display all the proteins in the protXML file that pass the ProteinProphet threshold and have ratios
protected void	errorMessage(java.lang.String message, java.lang.Throwable t) Display a dialog box with info message and stack trace
float	getMaxLowRatio()
float	getMinHighRatio()
float	getMinProteinProphet()
java.util.List<ProtXmlReader.Protein>	getSelectedProteins()
protected void	initGUI() Initialize GUI components
void	setMaxLowRatio(float maxLowRatio)
void	setMessage(java.lang.String message) Set status message.
void	setMinHighRatio(float minHighRatio)
void	setMinProteinProphet(float minProteinProphet)
void	setProteinGeneMap(java.util.Map<java.lang.String,java.util.List<java.lang.String>> proteinGeneMap) Define the mapping from protein names to gene symbols
void	setSelectedProteins(java.util.List<ProtXmlReader.Protein> selectedProteins)
protected void	updateExtremeRatioGUI() In response to a user action restricting ratios, modify what's shown on the table and reflected in the labels.

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

_log

protected static org.apache.log4j.Logger _log

width

protected int width

height

protected int height

TITLEBAR_HEIGHT

protected final int TITLEBAR_HEIGHT

See Also:

Constant Field Values

STATUSPANEL_HEIGHT

protected final int STATUSPANEL_HEIGHT

See Also:

Constant Field Values

SUMMARYPANEL_HEIGHT

protected final int SUMMARYPANEL_HEIGHT

See Also:

Constant Field Values

TABLEROW_HEIGHT

protected final int TABLEROW_HEIGHT

See Also:

Constant Field Values

LOGRATIO_HISTOGRAM_PANEL_HEIGHT

protected int LOGRATIO_HISTOGRAM_PANEL_HEIGHT

proteinSummaryTable

protected ProteinSummarySelectorFrame.ProteinSummaryTable proteinSummaryTable

tableSelectionModel

protected javax.swing.ListSelectionModel tableSelectionModel

selectedProteins

protected java.util.List<ProtXmlReader.Protein> selectedProteins

proteins

protected java.util.List<ProtXmlReader.Protein> proteins

proteinGroupNumberMap

protected java.util.Map<ProtXmlReader.Protein,java.lang.Integer> proteinGroupNumberMap

minProteinProphet

protected float minProteinProphet

minHighRatio

protected float minHighRatio

maxLowRatio

protected float maxLowRatio

allowMultipleSelection

protected boolean allowMultipleSelection

contentPanel

public javax.swing.JPanel contentPanel

summaryPanel

public javax.swing.JPanel summaryPanel

mainPanel

public javax.swing.JPanel mainPanel

logRatioHistogramPanel

public PanelWithLogRatioHistAndFields logRatioHistogramPanel

buttonShowEvents

protected javax.swing.JButton buttonShowEvents

buttonSaveTSV

protected javax.swing.JButton buttonSaveTSV

buttonSelectedProtein

protected javax.swing.JButton buttonSelectedProtein

buttonSelectAllVisible

protected javax.swing.JButton buttonSelectAllVisible

buttonDeselectAll

protected javax.swing.JButton buttonDeselectAll

statusPanel

public javax.swing.JPanel statusPanel

messageLabel

public javax.swing.JLabel messageLabel

maxLowRatioLabel

public javax.swing.JLabel maxLowRatioLabel

minHighRatioLabel

public javax.swing.JLabel minHighRatioLabel

numPassingProteinsLabel

public javax.swing.JLabel numPassingProteinsLabel

proteinGeneMap

protected java.util.Map<java.lang.String,java.util.List<java.lang.String>> proteinGeneMap

Constructor Detail

ProteinSummarySelectorFrame

public ProteinSummarySelectorFrame()

ProteinSummarySelectorFrame

public ProteinSummarySelectorFrame(boolean allowMultipleSelection)

ProteinSummarySelectorFrame

public ProteinSummarySelectorFrame(java.io.File protXmlFile)
                            throws javax.xml.stream.XMLStreamException,
                                   java.io.FileNotFoundException

Throws:

javax.xml.stream.XMLStreamException

java.io.FileNotFoundException

Method Detail

initGUI

protected void initGUI()

Initialize GUI components

setProteinGeneMap

public void setProteinGeneMap(java.util.Map<java.lang.String,java.util.List<java.lang.String>> proteinGeneMap)

Define the mapping from protein names to gene symbols

Parameters:

proteinGeneMap -

displayProteins

public void displayProteins(java.io.File protXmlFile)
                     throws javax.xml.stream.XMLStreamException,
                            java.io.FileNotFoundException,
                            java.lang.IllegalArgumentException

Display all the proteins in the protXML file that pass the ProteinProphet threshold and have ratios

Parameters:

protXmlFile -

Throws:

javax.xml.stream.XMLStreamException

java.io.FileNotFoundException

java.lang.IllegalArgumentException

updateExtremeRatioGUI

protected void updateExtremeRatioGUI()

In response to a user action restricting ratios, modify what's shown on the table and reflected in the labels. Called from two places

addSelectionListener

public void addSelectionListener(java.awt.event.ActionListener listener)

Add a listener for selecting a row in the table. This is used for populating the selected protein

Parameters:

listener -

buttonShowEvents_actionPerformed

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

Show the detail screen with a table of the actual events for this/these protein(s)

Parameters:

event -

buttonSelectAllVisible_actionPerformed

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

Select all currently-visible (i.e., passes filter) rows

Parameters:

event -

buttonDeselectAll_actionPerformed

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

Deselect all currently-selected rows, whether or not they're currently passing the filter

Parameters:

event -

buttonSaveTSV_actionPerformed

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

Save the table contents as a TSV file

Parameters:

event -

buttonCancel_actionPerformed

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

Quit

Parameters:

event -

displayProteins

public void displayProteins()

getSelectedProteins

public java.util.List<ProtXmlReader.Protein> getSelectedProteins()

setSelectedProteins

public void setSelectedProteins(java.util.List<ProtXmlReader.Protein> selectedProteins)

getMinProteinProphet

public float getMinProteinProphet()

setMinProteinProphet

public void setMinProteinProphet(float minProteinProphet)

setMessage

public void setMessage(java.lang.String message)

Set status message. Separate thread necessary or UI hangs

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 -

getMinHighRatio

public float getMinHighRatio()

setMinHighRatio

public void setMinHighRatio(float minHighRatio)

getMaxLowRatio

public float getMaxLowRatio()

setMaxLowRatio

public void setMaxLowRatio(float maxLowRatio)