Class SearchGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      SearchGUI

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class SearchGUI
extends javax.swing.JFrame
implements java.awt.event.ItemListener, java.awt.event.ActionListener, java.awt.event.WindowListener

Class SearchGUI is used to create a popup GUI to run the converter.

 List of Methods

 ===================
 SearchGUI() - Constructor
 initGUI() - create the popup GUI
 addMenuTree() - create pull down menus in menu bar for the GUI
 clearGuiProcessingState() - clear the GUI state
 processGuiStateData() - Process data specified by the GUI state
 resetGuiState() - reset the GUI state so nothing is specified.
 setCancelFlag() - set the Cancel flag value
 getCancelFlag() - get the Cancel flag value
 setDemoParameters() - set the Search Terms list for demo state.
 setUserTermListFromFile() - set  user search term-list state from a file.
 setGUItoSGstate() - set GUI to instance of SGstate.
 getGUItoSGstate() - get additional SGstate variables from GUI.
 setEnableSearchParamsButtonsAndMenus() - set Search Params GUI &  state
 setEnableCancelButtonsAndMenus() - when are able to do processing state
 setEnableViewingButtonsAndMenus() - enable view processed HTML files state
 positionReportWindow() - position report window on the screen
 setShow() - set the show/hide popup status
 updateReportStatusLine() - clear text in popup window
 clearText() - clear text in popup window
 getDBgeneList() - get printable text list of genes in the database.
 getEGsampleList() - get printable text list of EG samples in the database.
 matchEGsampleBySearchTerms() - test sGSPID if match searchTerms list.
 getReportText() - get the text from the Report popup window
 setReportText() - update text in popup window
 setGUItitle() - update title in popup window
 setSaveAsFile() - set SaveAs file default file name
 close() - close this popup and reset flags if needed
 testAndSetProjDir() - test and set project directory cvt.userDir.
 actionPerformed() - Handle menu actions and button clicks
 resetInitialGuiProcessingState() - reset search terms & samples GUI state
 quit() - closing down the window, get rid of the frame.
 updateSearchGUIjarFile() - update SearchGui.jar from URL_HOME web server.
 itemStateChanged() - handle item state changed events
 viewHTMLfile() - popup browser on guiActiveHTMLfile file.
 windowClosing() - closing down the window, get rid of the frame.
 
 Class SGstate - holds SearchGui GUI data that can be read/write by methods
 -------------
 SGstate() - constructor
 copyStateFromCvt() - copy the partial state from cvt Globals
 copySGstateInstance() - copy from SGstate instance values to this.
 cvtSGstateToStr() - convert SGstate vars. to .sgs state string to write to file.
 copyGlobalsToSGstate() - copy Globals instance in SGstate variables.
 readSGstateFile() - read the SearchGUI State file stateFile
 parseHTtoSGstate() - parse .sgs state hashtable to SGstate variables.
 writeSGstate() - write SearchGUI state to .sgs SGstate file.
 readNameValuesHashTableFromFile() - read hashtable tab-delim  name-value pairs
 setStateHashtableForGetValue() - set working hash table for next getStateValue calls
 getStateStr() - generate  tab-delim SGstate string for writing .sgs state.
 getStateValue() - get PARAM and use default if not found. 

This code is available at the HTMLtools project on SourceForge at http://htmltools.sourceforge.org/ under the "Common Public License Version 1.0" http://www.opensource.org/licenses/cpl1.0.php.

It was derived and refactored from the open source MAExplorer (http://maexplorer.sourceforge.org/), and Open2Dprot (http://Open2Dprot.sourceforge.net/) Table modules.

$Date: 2009/12/09 11:45:56 $ $Revision: 1.41 $
Copyright 2008, 2009 by Peter Lemkin E-Mail: lemkin@users.sourceforge.net http://lemkingroup.com/

See Also:

Serialized Form

Nested Class Summary

(package private) class

SearchGUI.SGstate Class SGstate contains the SearchGUI state as well as functions to maintain the state.

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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

private javax.swing.JRadioButton	andEGnamesRB AND match radio button for EG sample list specification, button grouped with orEGnamesRB.
PopupTextViewer	bptv Optional Big popup text viewer for Report-Log
javax.swing.JButton	cancelButton button for "Cancel" button - may enable/disable button
boolean	cancelFlag "Cancel" the processing in the GUI
private java.awt.MenuItem	classAMI MenuItem "Assign EG samples to Class A"
private java.awt.MenuItem	classBMI MenuItem "Assign EG samples to Class A"
boolean	closeGuiFlag "Close" the GUI
HTMLtools	cvt
private java.lang.String	dataSource The subtitle for generated Web page by mapping to the preface "$$DATA_SOURCE_SUBTITLE$$"
private java.lang.String[]	dbGSPIDlist This is the list of ftData Data Table columns starting with "EG" and is the list of EG GSP IDs in the database.
boolean	doneFlag "Done" processing data in the GUI
private java.awt.Menu	fileMenu "File" pull down Menu list
private javax.swing.JTextField	filterRowTextField
java.lang.String	flipTableDataFile Name of database Table file that we will use to verify search terms.
java.lang.String	flipTableIndexMapFile Name of Index Map file that we will use to verify search terms.
private java.awt.CheckboxMenuItem	foldChangeMCB Menu checkbox item for "Report Fold Change of 2 sample subsets"
private java.awt.CheckboxMenuItem	foldChangeThrMCB Menu checkbox item for "Only keep genes/probes with |fold-change| >= threshold" This pops up a dialog to enter the threshold value between 0.0 and some large number and saves it in sgs.foldChangeThr.
FileTable	ftData Header-only Data FileTable that we will use to get the list of EG Samples.We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
FileTable	ftIM Index Map FileTable that we will use to verify search terms.
java.lang.String	guiActiveHTMLfile
java.lang.String	guiActiveTXTfile
java.lang.String[]	guiArgV Command line string array created to use when running the converter used by ProcessDataSearch
java.lang.String	guiFSMstate GUI FSM state
java.lang.String	guiParamsMapDefaultPath GUI Converter params map default file path
java.lang.String	guiParamsMapFile GUI Converter params map file
private java.awt.Menu	helpMenu "Help" pull down Menu list
boolean	indexMapProblemFlag There has been a problem reading the Index Map file into ftIM by the ProcessLoadIndexMapData Thread.
boolean	indexMapReadyFlag The Index Map file into ftIM has been read successfully by the ProcessLoadIndexMapData Thread.
java.lang.String	inputSearchDir Param .map default input Dir
private java.awt.MenuItem	lastRestoreSGstateMI MenuItem "Restore previously saved search .sgs parameters from file"
private java.awt.Menu	listMenu "List" pull down Menu list
private javax.swing.JRadioButton	matchGeneTermRB Exact match radio button for search-term specification, button grouped with matchSearchStrTermRB.
private javax.swing.JRadioButton	matchSubStrTermRB Substring match radio button for search-term specification, button grouped with matchGeneTermRB.
private java.awt.MenuBar	mbar menu bar for the frame
private MenuSupport	ms Menu support functions using Hashtables to track what is active
private int	nSearchTermNames
private javax.swing.JRadioButton	orEGnamesRB OR match radio button for EG sample list specification, button grouped with andEGnamesRB.
java.lang.String	outputSearchDir Param .map default output Dir
ProcessDataSearch	pds Thread for converter processing
javax.swing.JButton	processButton button for "Process" button - may enable/disable button
boolean	processedOKflag "Process was ok" if true.
boolean	processFlag "Processing" data in the GUI
private java.lang.String	programName The name of the program
private java.lang.String	reportFile Default SAVE AS .txt file for Report-Log textReport data used in reportTextarea.
private javax.swing.JTextArea	reportTextarea Text area GUI for main Report-Log.
private javax.swing.JButton	resetButton button for "Reset" converter button
private java.awt.MenuItem	restoreSGstateMI MenuItem "Restore previously saved search .sgs parameters from file"
private java.lang.String[][]	sampleChoiceData The sample list is a 2 column array where the Object value is [][0], and the viewable choice name is [][1].
private javax.swing.JList	samplesList
private java.awt.MenuItem	saveSGstateMI MenuItem "SaveAs current search .sgs parameters to file"
private javax.swing.JTextField	searchResultsFilenamePrefixTF SearchResults filename Prefix text field
private java.lang.String	searchRowFilterName Switch supplied search sample groups filter name for sampleExprGroupsTextArea.
private java.lang.String	searchRowFilterPrompt Switch supplied search samples group filter prompt for sampleExprGroupsTextArea.
private java.lang.String	searchSampleChoiceFile The name of the sample list Table file.
private java.lang.String[][]	searchTermFilter
private java.lang.String[]	searchTermNames
private java.lang.String	searchTermsFilterPrompt Switch supplied search Terms filter prompt for searchTermTextArea Set by -searchTermsFilterPrompt:{...}.
private javax.swing.JTextArea	searchTermTextArea Text area GUI for entering list of search terms
static long	serialVersionUID
SearchGUI.SGstate	sgs SearchGUI state variables that can be saved/imported from .sgs files.
SearchGUI	sGui
java.lang.String	sGuiArgV Command line string created to use when running the converter used by ProcessDataSearch
private java.awt.CheckboxMenuItem	showDataHeatmapFlipTableMCB Menu checkbox item for "Show data heat-map in View HTML Results"
boolean	showStatusFlag
private javax.swing.JLabel	statusLineLabel Status line label updated with UtilCM.updateReportStatusLine()
java.lang.String	tableSearchDir Param .map default table Dir
private int	textAreaFontSize font size
private java.lang.String	textFontFamily Text area font family
private java.lang.String	textReport Copy of text in Report-Log reportTextarea
private java.lang.String	title string for title of frame
static java.lang.String	URL_HOME Home URL for server
static java.lang.String	URL_JAR_FILE URL for SearchGui.jar if update from the server
private java.awt.CheckboxMenuItem	verboseMCB Menu checkbox item for Verbose reporting
private java.lang.String	version version number of the program
javax.swing.JButton	viewHTMLButton button for "ViewHTML" button - may enable/disable button
private java.awt.Menu	viewMenu "View" pull down Menu list

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

SearchGUI(HTMLtools cvt, java.lang.String programName, java.lang.String version, java.lang.String textReport, java.lang.String title, java.lang.String reportFile, java.lang.String paramsMapDefaultFile)
SearchGUI() - Constructor

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle menu actions and button clicks
private void	addMenuTree(java.awt.Frame f, java.awt.MenuBar mbar) addMenuTree() - create pull down menus in menu bar for the GUI
void	clearGuiProcessingState() clearGuiProcessingState() - clear the GUI state
void	clearText() clearText() - clear text in popup window
void	close() close() - close this popup and reset flags if needed
private boolean	createParamsMapFile() createParamsMapFile() - Create guiParamsMapFile from default params.map file
boolean	getCancelFlag() getCancelFlag() - get the Cancel flag value
java.lang.String	getDBgeneList(java.lang.String searchTermsStr, boolean matchSubstringFlag) getDBgeneList() - get printable text list of genes in the database.
java.lang.String	getEGclassSampleList(java.lang.String classSamplesList, java.lang.String className, java.lang.String sTitle) getEGclassSampleList() - get printable text list of class EG samples.
java.lang.String	getEGsampleList(java.lang.String searchTermsStr, java.lang.String[] egGroupList, boolean evalSchANDboolean, java.lang.String sTitle) getEGsampleList() - get printable text list of EG samples in the database.
java.lang.String	getEGsamplesString(java.lang.String searchTermsStr, java.lang.String[] egGroupList, boolean evalSchANDboolean) getEGsamplesString() - get "," separated text string of EG samples in database.
java.lang.String	getGuiFSM() getGuiFSM() - Get the GUI FSM state string.
private boolean	getGUItoSGstate(SearchGUI.SGstate sg) getGUItoSGstate() - get additional SGstate variables from GUI.
boolean	getOtherSearchParams(java.lang.String paramsSearchDefaultPath) getOtherSearchParams() - get search information for GUI for prompts and menus These terms are found in the default search params .map file.
java.lang.String	getReportText() getReportText() - get the text from the Report popup window
void	getSearchResultsFilenamePrefix() getSearchResultsFilenamePrefix() - get the new value from JTextField searchResultsFilenamePrefixTF and set it to searchResultsBaseFile
boolean	initGUI() initGUI() - create the popup GUI
void	itemStateChanged(java.awt.event.ItemEvent e) itemStateChanged() - handle item state changed events NOTE: need to implement CheckboxMenuItems.
private boolean	matchEGsampleBySearchTerms(java.lang.String sGSPID, java.lang.String[] searchTermList, boolean evalSchANDboolean) matchEGsampleBySearchTerms() - test sGSPID if match searchTerms list.
void	positionReportWindow() positionReportWindow() - position report window on the screen
void	printGuiFSM(java.lang.String preface, boolean printFlag) printGuiFSM() - print GuiFSM if printFlag set
void	printGuiFSMlf(java.lang.String preface, boolean printFlag) printGuiFSMlf() - print GuiFSM if printFlag set followed by extra line feed
private void	printSearchResultsFileNames() printSearchResultsFileNames() - print Search-Results File Names to log.
private boolean	processGuiStateData() processGuiStateData() - Process data specified by the GUI state.
void	quit() quit() - closing down the window, get rid of the frame.
void	resetInitialGuiProcessingState() resetInitialGuiProcessingState() - reset the search terms & samples GUI state
private boolean	restoreGUIfromGSstateFile(java.lang.String filePath) restoreGUIfromGSstateFile() - restore GUI from GSstate .sgs file
private boolean	saveGUItoGSstateFile(java.lang.String filePath) saveGUItoGSstateFile() - save GUI to GSstate .sgs file
void	setCancelFlag(boolean flag) setCancelFlag() - set the Cancel flag value
void	setDemoParameters() setDemoParameters() - set the Search Terms list for demo state.
void	setEnableCancelButtonsAndMenus(java.lang.String statusLabel) setEnableCancelButtonsAndMenus() - when are able to do processing state.
void	setEnableCancelState() setEnableCancelState() - when are able to do processing state.
void	setEnableSearchParamsButtonsAndMenus() setEnableSearchParamsButtonsAndMenus() - set Search buttons & menus state.
void	setEnableSearchParamsState() setEnableSearchParamsState() - set Search parameters GUI & menus state.
void	setEnableViewingButtonsAndMenus() setEnableViewingButtonsAndMenus() - when can view processed HTML files state.
void	setEnableViewingState() setEnableViewingState() - when can view processed HTML files state.
void	setGUItitle(java.lang.String title) setGUItitle() - update title in popup window
private boolean	setGUItoSGstate(SearchGUI.SGstate sg) setGUItoSGstate() - set GUI to instance of SGstate.
void	setReportText(java.lang.String newText) setReportText() - update text in popup window
void	setSaveAsFile(java.lang.String reportFile) setSaveAsFile() - set SaveAs file default file name
void	setShow(boolean showStatusFlag) setShow() - set the show/hide popup status
void	setUserSearchTermFileParameters() setUserSearchTermFileParameters() - set search term list from user file.
boolean	setUserTermListFromFile() setUserTermListFromFile() - set user search term-list state from a file.
java.lang.String	testAndSetProjDir(java.lang.String testProjDir, boolean fatalFlag) testAndSetProjDir() - test and set project directory cvt.userDir.
void	updateReportStatusLine(java.lang.String msg) updateReportStatusLine() - clear text in popup window
void	updateSampleList(javax.swing.event.ListSelectionEvent lsEvent) updateSampleList() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.
boolean	updateSearchGUIjarFile() updateSearchGUIjarFile() - update the SearchGui.jar file from the URL_HOME web server.
private boolean	viewHTMLfile() viewHTMLfile() - popup browser on guiActiveHTMLfile file.
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - closing down the window, get rid of the frame.
void	windowDeactivated(java.awt.event.WindowEvent e)
void	windowDeiconified(java.awt.event.WindowEvent e)
void	windowIconified(java.awt.event.WindowEvent e)
void	windowOpened(java.awt.event.WindowEvent e)

Methods inherited from class javax.swing.JFrame

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

Methods inherited from class java.awt.Frame

addNotify, finalize, 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, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, 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, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, 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, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

URL_HOME

public static final java.lang.String URL_HOME

Home URL for server

See Also:

Constant Field Values

URL_JAR_FILE

public static final java.lang.String URL_JAR_FILE

URL for SearchGui.jar if update from the server

See Also:

Constant Field Values

cvt

public HTMLtools cvt

sGui

public SearchGUI sGui

sgs

public SearchGUI.SGstate sgs

SearchGUI state variables that can be saved/imported from .sgs files.

title

private java.lang.String title

string for title of frame

programName

private java.lang.String programName

The name of the program

version

private java.lang.String version

version number of the program

mbar

private java.awt.MenuBar mbar

menu bar for the frame

fileMenu

private java.awt.Menu fileMenu

"File" pull down Menu list

viewMenu

private java.awt.Menu viewMenu

"View" pull down Menu list

listMenu

private java.awt.Menu listMenu

"List" pull down Menu list

helpMenu

private java.awt.Menu helpMenu

"Help" pull down Menu list

ms

private MenuSupport ms

Menu support functions using Hashtables to track what is active

verboseMCB

private java.awt.CheckboxMenuItem verboseMCB

Menu checkbox item for Verbose reporting

foldChangeMCB

private java.awt.CheckboxMenuItem foldChangeMCB

Menu checkbox item for "Report Fold Change of 2 sample subsets"

foldChangeThrMCB

private java.awt.CheckboxMenuItem foldChangeThrMCB

Menu checkbox item for "Only keep genes/probes with |fold-change| >= threshold" This pops up a dialog to enter the threshold value between 0.0 and some large number and saves it in sgs.foldChangeThr. The associated flag is sgs.foldChangeThrFlag.

lastRestoreSGstateMI

private java.awt.MenuItem lastRestoreSGstateMI

MenuItem "Restore previously saved search .sgs parameters from file"

restoreSGstateMI

private java.awt.MenuItem restoreSGstateMI

MenuItem "Restore previously saved search .sgs parameters from file"

saveSGstateMI

private java.awt.MenuItem saveSGstateMI

MenuItem "SaveAs current search .sgs parameters to file"

classAMI

private java.awt.MenuItem classAMI

MenuItem "Assign EG samples to Class A"

classBMI

private java.awt.MenuItem classBMI

MenuItem "Assign EG samples to Class A"

showDataHeatmapFlipTableMCB

private java.awt.CheckboxMenuItem showDataHeatmapFlipTableMCB

Menu checkbox item for "Show data heat-map in View HTML Results"

showStatusFlag

public boolean showStatusFlag

textAreaFontSize

private int textAreaFontSize

font size

textFontFamily

private java.lang.String textFontFamily

Text area font family

bptv

public PopupTextViewer bptv

Optional Big popup text viewer for Report-Log

reportTextarea

private javax.swing.JTextArea reportTextarea

Text area GUI for main Report-Log. Data is also kept int textReport and can be saved in reportFile.

searchTermTextArea

private javax.swing.JTextArea searchTermTextArea

Text area GUI for entering list of search terms

samplesList

private javax.swing.JList samplesList

processButton

public javax.swing.JButton processButton

button for "Process" button - may enable/disable button

cancelButton

public javax.swing.JButton cancelButton

button for "Cancel" button - may enable/disable button

viewHTMLButton

public javax.swing.JButton viewHTMLButton

button for "ViewHTML" button - may enable/disable button

resetButton

private javax.swing.JButton resetButton

button for "Reset" converter button

statusLineLabel

private javax.swing.JLabel statusLineLabel

Status line label updated with UtilCM.updateReportStatusLine()

filterRowTextField

private javax.swing.JTextField filterRowTextField

searchResultsFilenamePrefixTF

private javax.swing.JTextField searchResultsFilenamePrefixTF

SearchResults filename Prefix text field

matchGeneTermRB

private javax.swing.JRadioButton matchGeneTermRB

Exact match radio button for search-term specification, button grouped with matchSearchStrTermRB. Sets sgs.flipTableUseExactMatchFlag.

matchSubStrTermRB

private javax.swing.JRadioButton matchSubStrTermRB

Substring match radio button for search-term specification, button grouped with matchGeneTermRB. Clears sgs.flipTableUseExactMatchFlag.

andEGnamesRB

private javax.swing.JRadioButton andEGnamesRB

AND match radio button for EG sample list specification, button grouped with orEGnamesRB. Sets sgs.evalSearchANDbooleanFlag.

orEGnamesRB

private javax.swing.JRadioButton orEGnamesRB

OR match radio button for EG sample list specification, button grouped with andEGnamesRB. Clears sgs.evalSearchANDbooleanFlag.

textReport

private java.lang.String textReport

Copy of text in Report-Log reportTextarea

reportFile

private java.lang.String reportFile

Default SAVE AS .txt file for Report-Log textReport data used in reportTextarea.

searchTermsFilterPrompt

private java.lang.String searchTermsFilterPrompt

Switch supplied search Terms filter prompt for searchTermTextArea Set by -searchTermsFilterPrompt:{...}.

searchTermFilter

private java.lang.String[][] searchTermFilter

searchTermNames

private java.lang.String[] searchTermNames

nSearchTermNames

private int nSearchTermNames

flipTableDataFile

public java.lang.String flipTableDataFile

Name of database Table file that we will use to verify search terms. We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.

flipTableIndexMapFile

public java.lang.String flipTableIndexMapFile

Name of Index Map file that we will use to verify search terms. We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'. This is used to read the ftIM FileTable.

ftIM

public FileTable ftIM

Index Map FileTable that we will use to verify search terms. We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.

ftData

public FileTable ftData

Header-only Data FileTable that we will use to get the list of EG Samples.We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.

dbGSPIDlist

private java.lang.String[] dbGSPIDlist

This is the list of ftData Data Table columns starting with "EG" and is the list of EG GSP IDs in the database.

indexMapReadyFlag

public volatile boolean indexMapReadyFlag

The Index Map file into ftIM has been read successfully by the ProcessLoadIndexMapData Thread.

indexMapProblemFlag

public volatile boolean indexMapProblemFlag

There has been a problem reading the Index Map file into ftIM by the ProcessLoadIndexMapData Thread.

searchSampleChoiceFile

private java.lang.String searchSampleChoiceFile

The name of the sample list Table file. It is a 2 column array where used for the sample Choice GUI where the choice Object value is [][0], and the viewable choice name is [][1]. Set by '-searchsearchSampleChoiceFile:{sample choice Table file}'.

sampleChoiceData

private java.lang.String[][] sampleChoiceData

The sample list is a 2 column array where the Object value is [][0], and the viewable choice name is [][1].

searchRowFilterName

private java.lang.String searchRowFilterName

Switch supplied search sample groups filter name for sampleExprGroupsTextArea. Set by -searchRowFilterName:{...}.

searchRowFilterPrompt

private java.lang.String searchRowFilterPrompt

Switch supplied search samples group filter prompt for sampleExprGroupsTextArea. Set by -searchRowFilterPrompt:{...}.

pds

public ProcessDataSearch pds

Thread for converter processing

processFlag

public volatile boolean processFlag

"Processing" data in the GUI

processedOKflag

public volatile boolean processedOKflag

"Process was ok" if true. Set to false if any problems.

doneFlag

public volatile boolean doneFlag

"Done" processing data in the GUI

closeGuiFlag

public volatile boolean closeGuiFlag

"Close" the GUI

cancelFlag

public volatile boolean cancelFlag

"Cancel" the processing in the GUI

guiFSMstate

public volatile java.lang.String guiFSMstate

GUI FSM state

dataSource

private java.lang.String dataSource

The subtitle for generated Web page by mapping to the preface "$$DATA_SOURCE_SUBTITLE$$"

inputSearchDir

public volatile java.lang.String inputSearchDir

Param .map default input Dir

outputSearchDir

public volatile java.lang.String outputSearchDir

Param .map default output Dir

tableSearchDir

public volatile java.lang.String tableSearchDir

Param .map default table Dir

guiParamsMapFile

public volatile java.lang.String guiParamsMapFile

GUI Converter params map file

guiParamsMapDefaultPath

public volatile java.lang.String guiParamsMapDefaultPath

GUI Converter params map default file path

guiActiveHTMLfile

public volatile java.lang.String guiActiveHTMLfile

guiActiveTXTfile

public volatile java.lang.String guiActiveTXTfile

sGuiArgV

public volatile java.lang.String sGuiArgV

Command line string created to use when running the converter used by ProcessDataSearch

guiArgV

public volatile java.lang.String[] guiArgV

Command line string array created to use when running the converter used by ProcessDataSearch

Constructor Detail

SearchGUI

public SearchGUI(HTMLtools cvt,
                 java.lang.String programName,
                 java.lang.String version,
                 java.lang.String textReport,
                 java.lang.String title,
                 java.lang.String reportFile,
                 java.lang.String paramsMapDefaultFile)

SearchGUI() - Constructor

Parameters:

cvt - is an instance of the CvtTabDelim2HTML class

programName - name of the program

version - - of program

textReport - is initial text string for buffer.

title - of the window

String - reportFile is default SAVE AS .txt file. Default "log.txt"

guiParamsMapDefaultFile - is default params. map file if not null, else it uses "paramsSearchDefault.map".

Method Detail

getOtherSearchParams

public boolean getOtherSearchParams(java.lang.String paramsSearchDefaultPath)

getOtherSearchParams() - get search information for GUI for prompts and menus These terms are found in the default search params .map file. The following must be defined:

 E.g.,
   -flipTableByIndexMap:{dataSet.txt,dataSet.idx}
   -searchTermNames:"Gene,Feature ID"
   -searchRowFilterName:"Sample Experiment Groups"
   -searchSampleChoiceFile:sampleExperimentGroupsChoices.txt
   -searchTermsDemoData:"Stat5a Stat5b 1438470_at 1441476_at 1446085_at"
   -searchUserTermList:"LitRefGeneList.txt,Gene,Literature Review"
   -searchTermsFilterPrompt:"'Gene' and/or 'Probe' names. E.g., Stat5a, Stat5b, 1449109_at, etc."
   -searchRowFilterPrompt:"'Sample Experiment Groups'. E.g., select one or more Experiment Groups"

Returns:

true if succeed, false if do not find all of the search terms

initGUI

public boolean initGUI()

initGUI() - create the popup GUI

Returns:

true if succeed

addMenuTree

private void addMenuTree(java.awt.Frame f,
                         java.awt.MenuBar mbar)

addMenuTree() - create pull down menus in menu bar for the GUI

Parameters:

f - is frame

mbar - is MenuBar

processGuiStateData

private boolean processGuiStateData()

processGuiStateData() - Process data specified by the GUI state. This is called from the "Process" event-handler for the button and menu handler.

Returns:

true if succeed, false if any problems after write err msg to window

createParamsMapFile

private boolean createParamsMapFile()

createParamsMapFile() - Create guiParamsMapFile from default params.map file

 Add the following required switches:
   -flipOrderHdrColNames:"*LIST*,Stat5a,"
   -flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
   -flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at"
   -flipRowFilterNames:\"*LIST*,EG003.1,EG003.2"
  
 Add the following optional switches:
   -flipRowGSPIDfilterSubstring:"AND,.stat,.GH"
   -flipAclass:"{classAsamples}"  [if sgs.reportFoldChangeFlag]
   -flipBclass:"{classBsamples}"  [if sgs.reportFoldChangeFlag]
   -flipFCthreshold:{foldChangeThr} [if foldChangeThrFlag && foldChangeThr>0.0F]
   -dataPrecisionHTMLtable:{precision of HTML table}
   -sortFlipTableByColumnName:{sort column}
   -showDataHeatmapFlipTable
   -flipUseExactColumnNameMatch:{sgs.flipTableUseExactMatchFlag}
   -flipDirectory:"{outputSearchDir}"
   -flipSaveOutputFile:"{searchResultsBaseFile}"
 

Returns:

true if created the params .map file

setDemoParameters

public void setDemoParameters()

setDemoParameters() - set the Search Terms list for demo state. The demo argument to load into the searchTermTextArea GUI Set by "-searchTermsDemoData:{list of search terms}" The demo argument to load into the sample list choice GUI and into sampleRowFilter[] data. Set by "-searchRowsDemoData:{list of sample groups}"

setUserSearchTermFileParameters

public void setUserSearchTermFileParameters()

setUserSearchTermFileParameters() - set search term list from user file. The demo argument to load into the searchTermTextArea GUI Set by "-searchUserTermList:{userListTable,colName,title string}". The demo argument to load into the sample list choice GUI.

setUserTermListFromFile

public boolean setUserTermListFromFile()

setUserTermListFromFile() - set user search term-list state from a file. It pops up a file browser with the default set to {userListTable} which can be a single column list or if a Table, then use the {colName} set by "-searchUserTermList:{userListTable,colName,title str}". If {colName} is not specified, then assume the data is just delimited search terms. Map all " ", ",", "\t" and "\n" to single space normalized string. The list is then loaded into the searchTermTextArea GUI

setGUItoSGstate

private boolean setGUItoSGstate(SearchGUI.SGstate sg)

setGUItoSGstate() - set GUI to instance of SGstate. Set the GUI to variables in SGstate sg instance.

Parameters:

sg - is instance of SGstate to use (that could be different than this.sgs

Returns:

true if succeed

getGUItoSGstate

private boolean getGUItoSGstate(SearchGUI.SGstate sg)

getGUItoSGstate() - get additional SGstate variables from GUI. Note that most variables are set as the GUI state changes, but some sg variables need to be set. I.e., the TextAreas and TextFields. Set the GUI to variables in SGstate sg instance.

Parameters:

sg - is instance of SGstate to use (that could be different than this.sgs

Returns:

true if succeed

saveGUItoGSstateFile

private boolean saveGUItoGSstateFile(java.lang.String filePath)

saveGUItoGSstateFile() - save GUI to GSstate .sgs file

Parameters:

filePath - - of .sgs file to save

Returns:

true if succeed

restoreGUIfromGSstateFile

private boolean restoreGUIfromGSstateFile(java.lang.String filePath)

restoreGUIfromGSstateFile() - restore GUI from GSstate .sgs file

Parameters:

filePath - - of .sgs file to restore

Returns:

true if succeed

setEnableSearchParamsButtonsAndMenus

public void setEnableSearchParamsButtonsAndMenus()

setEnableSearchParamsButtonsAndMenus() - set Search buttons & menus state. This sets the flags to the initial "Assign" data state.

setEnableCancelButtonsAndMenus

public void setEnableCancelButtonsAndMenus(java.lang.String statusLabel)

setEnableCancelButtonsAndMenus() - when are able to do processing state. This sets the flags to the "Process" data state. It also clears the list of generated HTML files.

Parameters:

statusLabel - to use for Report status line.

setEnableViewingButtonsAndMenus

public void setEnableViewingButtonsAndMenus()

setEnableViewingButtonsAndMenus() - when can view processed HTML files state. This sets the flags to the "Viewing-enable" data state.

positionReportWindow

public void positionReportWindow()

positionReportWindow() - position report window on the screen

setShow

public void setShow(boolean showStatusFlag)

setShow() - set the show/hide popup status

Parameters:

showStatusFlag - to show (true), hide(false).

updateReportStatusLine

public void updateReportStatusLine(java.lang.String msg)

updateReportStatusLine() - clear text in popup window

Parameters:

msg - to display

clearText

public void clearText()

clearText() - clear text in popup window

getReportText

public java.lang.String getReportText()

getReportText() - get the text from the Report popup window

Returns:

text report

getSearchResultsFilenamePrefix

public void getSearchResultsFilenamePrefix()

getSearchResultsFilenamePrefix() - get the new value from JTextField searchResultsFilenamePrefixTF and set it to searchResultsBaseFile

getDBgeneList

public java.lang.String getDBgeneList(java.lang.String searchTermsStr,
                                      boolean matchSubstringFlag)

getDBgeneList() - get printable text list of genes in the database. If there are no search terms, then return the entire list.

Parameters:

searchTermsStr - - list of search terms if not null in which case return the entire list

matchSubstringFlag - - to match it as a substring of Gene field, else use the exact match.

Returns:

text if found, else "" if a problem.

getEGsampleList

public java.lang.String getEGsampleList(java.lang.String searchTermsStr,
                                        java.lang.String[] egGroupList,
                                        boolean evalSchANDboolean,
                                        java.lang.String sTitle)

getEGsampleList() - get printable text list of EG samples in the database. If there are no search terms, then return the entire list. [TODO] Read the header from the Database file which contains the sample GSP IDs but omit the leading "Gene, Well ID, Feature ID"

Parameters:

searchTermsStr - - list of search terms if not null in which case return the entire list,

egGroupList - - is list of the EG groups, if ALL, then all groups

evalSchANDboolean - - is true if AND, false if OR for matching search terms.

sTitle - optional title if not null

Returns:

text if found, else "" if a problem.

getEGclassSampleList

public java.lang.String getEGclassSampleList(java.lang.String classSamplesList,
                                             java.lang.String className,
                                             java.lang.String sTitle)

getEGclassSampleList() - get printable text list of class EG samples.

Parameters:

classSamplesList - - set of comma-delim. Class A or B EG samples

className - - (e.g., "A" or "B")

sTitle - - optional title

Returns:

printable list else null.

getEGsamplesString

public java.lang.String getEGsamplesString(java.lang.String searchTermsStr,
                                           java.lang.String[] egGroupList,
                                           boolean evalSchANDboolean)

getEGsamplesString() - get "," separated text string of EG samples in database. If there are no search terms, then return the entire list. [TODO] Read the header from the Database file which contains the sample GSP IDs but omit the leading "Gene, Well ID, Feature ID"

Parameters:

searchTermsStr - - list of search terms if not null in which case return the entire list,

egGroupList - - is list of the EG groups, if ALL, then all groups

evalSchANDboolean - - is true if AND, false if OR for matching search terms.

Returns:

text if found, else "" if a problem.

matchEGsampleBySearchTerms

private boolean matchEGsampleBySearchTerms(java.lang.String sGSPID,
                                           java.lang.String[] searchTermList,
                                           boolean evalSchANDboolean)

matchEGsampleBySearchTerms() - test sGSPID if match searchTerms list. Match by evalSearchANDbooleanFlag true if AND, false if OR for matching search terms.

Parameters:

sGSPID - - EG sample GSP ID name

searchTerms - - list of search terms to test

evalSchANDboolean - - is true if AND, false if OR for matching search terms.

Returns:

true if match successful.

setReportText

public void setReportText(java.lang.String newText)

setReportText() - update text in popup window

Parameters:

newText - is string to copy into text window

setGUItitle

public void setGUItitle(java.lang.String title)

setGUItitle() - update title in popup window

Parameters:

title - is new title.

setSaveAsFile

public void setSaveAsFile(java.lang.String reportFile)

setSaveAsFile() - set SaveAs file default file name

Parameters:

reportFile - is new reportFile.

close

public void close()

close() - close this popup and reset flags if needed

testAndSetProjDir

public java.lang.String testAndSetProjDir(java.lang.String testProjDir,
                                          boolean fatalFlag)

testAndSetProjDir() - test and set project directory cvt.userDir. If valid, then save it in cvt.userDir. [TODO] need to [DEBUG]

Parameters:

testProjDir - project directory

Returns:

projDir if succeed in finding the project directory, else null

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

actionPerformed() - Handle menu actions and button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - is action evet

printSearchResultsFileNames

private void printSearchResultsFileNames()

printSearchResultsFileNames() - print Search-Results File Names to log.

printGuiFSM

public void printGuiFSM(java.lang.String preface,
                        boolean printFlag)

printGuiFSM() - print GuiFSM if printFlag set

printGuiFSMlf

public void printGuiFSMlf(java.lang.String preface,
                          boolean printFlag)

printGuiFSMlf() - print GuiFSM if printFlag set followed by extra line feed

getGuiFSM

public java.lang.String getGuiFSM()

getGuiFSM() - Get the GUI FSM state string.

Returns:

the current state string

resetInitialGuiProcessingState

public void resetInitialGuiProcessingState()

resetInitialGuiProcessingState() - reset the search terms & samples GUI state

clearGuiProcessingState

public void clearGuiProcessingState()

clearGuiProcessingState() - clear the GUI state

setCancelFlag

public void setCancelFlag(boolean flag)

setCancelFlag() - set the Cancel flag value

Parameters:

flag - value to set the cancelFlag

getCancelFlag

public boolean getCancelFlag()

getCancelFlag() - get the Cancel flag value

setEnableSearchParamsState

public void setEnableSearchParamsState()

setEnableSearchParamsState() - set Search parameters GUI & menus state. This sets the flags to the initial "SearchParams" data state.

setEnableCancelState

public void setEnableCancelState()

setEnableCancelState() - when are able to do processing state. This sets the flags to the "Process" data state. It also clears the list of generated HTML files.

setEnableViewingState

public void setEnableViewingState()

setEnableViewingState() - when can view processed HTML files state. This sets the flags to the "Viewing-enable" data state.

quit

public void quit()

quit() - closing down the window, get rid of the frame.

See Also:

close()

updateSearchGUIjarFile

public boolean updateSearchGUIjarFile()

updateSearchGUIjarFile() - update the SearchGui.jar file from the URL_HOME web server.

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)

itemStateChanged() - handle item state changed events NOTE: need to implement CheckboxMenuItems.

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

Parameters:

e - is ItemEvent

updateSampleList

public void updateSampleList(javax.swing.event.ListSelectionEvent lsEvent)

updateSampleList() - handle item state changed events NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and CheckboxMenuItems.

Parameters:

e - is ItemEvent

viewHTMLfile

private boolean viewHTMLfile()

viewHTMLfile() - popup browser on guiActiveHTMLfile file.

Returns:

true if succeed

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

windowClosing() - closing down the window, get rid of the frame.

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - is window closing event

See Also:

close()

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener