Class PopupGeneGuesser

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Window
                    |
                    +--java.awt.Frame
                          |
                          +--Guesser
                                |
                                +--PopupGeneGuesser

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, java.awt.event.FocusListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.awt.event.WindowListener

class PopupGeneGuesser

extends Guesser

The PopupGeneGuesser class is a popup gene name/genomic ID gene guesser. Data is matched independent of case (all data is converted to upper-case for conversion purposes). This class is initialized during startup and the gene names and Master Gene IDs are sorted at that time so they are ready to go if the guesser is ever invoked. It is used in either of two ways:

   1) define the current gene - by pressing the "Done" button
   2) to set the genes matching a substring or wild card substring to the
      Edited Gene List (EGL) -  by pressing the "Set E.G.L" button.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/04/03 21:03:29 $ $Revision: 1.6 $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home, Guesser, Serialized Form

Inner classes inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Inner classes inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Inner classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Inner classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock

Field Summary

(package private) static int	DEF_GNMID_TA_COLS default size of text area
(package private) static int	DEF_GNMID_TA_ROWS default size of text area
(package private) boolean	doubleListFlag numeric/alpha or alpha only
(package private) static java.lang.String[]	geneNameList unsorted list of geneName, is G.C.'ed
(package private) static int	geneNameListSize unsorted list of geneName size
(package private) static java.lang.String	guesserTitle title for window
(package private) static java.lang.String[]	masterIDList unsorted list of clone_id, is G.C.'ed
(package private) static int	masterIDListSize unsorted list of clone_id size
(package private) static java.lang.String	sortedClassIDListStr sorted list of clone_id
(package private) static java.lang.String	sortedGeneNameListStr sorted list of geneName
(package private) boolean	strDataIsSortedFlag set once it is sorted
(package private) int	taCols default size of text area
(package private) int	taRows default size of text area

Fields inherited from class Guesser

alphaList, alphaListMode, alphaListSize, BAD_MODE, buttonPanel, chFirstTyped, DEF_GUESSER_DISP_SIZE, DEF_TA_COLS, DEF_TA_ROWS, font, frame, geneDBnamesButton, geneIDname, genericFlag, gipo, iMode, kev, mae, map, maxGenes, mbf, meh, MODE_DB_EST3, MODE_DB_EST5, MODE_GENBANK, MODE_GENBANK3, MODE_GENBANK5, MODE_LOCUSLINK, MODE_MASTER_GENE_NAME, MODE_MASTER_ID, MODE_SWISSPROT, MODE_UNIGENE, MULTIPLE_GENE, onceOnlyFlag, pgcg, phpmg, pPDg, resultMode, resultStr, resultSubList, setEGLfromListFlag, SINGLE_GENE, sortedAlphaListStr, subAlphaList, ta, tf, title, titleLabel, titlePanel

Fields inherited from class java.awt.Frame

base, CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, frameSerializedDataVersion, HAND_CURSOR, icon, ICONIFIED, mbManagement, menuBar, MOVE_CURSOR, N_RESIZE_CURSOR, nameCounter, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, ownedWindows, resizable, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, serialVersionUID, state, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR, weakThis

Fields inherited from class java.awt.Window

active, dbg, focusMgr, inputContext, inputContextLock, OPENED, ownedWindowList, showWithParent, warningString, windowListener, windowSerializedDataVersion

Fields inherited from class java.awt.Container

component, containerListener, containerSerializedDataVersion, dispatcher, layoutMgr, listeningBoundsChildren, listeningChildren, maxSize, ncomponents, printing, printingThreads

Fields inherited from class java.awt.Component

accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, name, nameExplicitlySet, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, privateKey, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

(package private)

PopupGeneGuesser(MAExplorer maE, char chFirstTyped, java.awt.Font font) PopupGeneGuesser() - constructor

Method Summary

(package private) void	cancel() cancel() - cancel the guesser window
(package private) void	clear() clear() - clear the text field in the main window
(package private) void	done(java.lang.String resultStr) done() - process the selected text, set current gene, and then popdown the guesser
private static void	preSortLists(MAExplorer mae) preSortLists() - presort lists of Gene_Name and Master_ID for Guesser It copies the Gene data into the working geneNameList[] and the masterIDList[] with sizes geneNameListSize, masterIDListSize .
(package private) void	setEGL(java.lang.String[] resultsList, java.lang.String resultStr) setEGL() - process the selected text for setting EGL, popdown the guesser
(package private) static void	sortGeneNameAndCloneIDLists(MAExplorer mae) sortGeneNameAndCloneIDLists() - sort lists of Master_IDs & Gene_Names for use with the guesser.
(package private) void	updateAssocTextField(java.lang.String str) updateAssocTextField() - update the associated text field
(package private) void	updateAssocTextFieldCaretPos(int pos) updateAssocTextFieldCaretPos() - update assoc text field caret position

Methods inherited from class Guesser

actionPerformed, buildAndRunGuesser, clearData, close, copyArrayToSizedArray, focusGained, focusLost, handleKeyTyped, setData, switchAlphaList, wildCard, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.awt.Frame

, addNotify, addToFrameList, constructComponentName, finalize, getAccessibleContext, getCursorType, getFrames, getIconImage, getMenuBar, getState, getTitle, initIDs, isResizable, paramString, postProcessKeyEvent, readObject, remove, removeFromFrameList, removeNotify, setCursor, setIconImage, setMenuBar, setResizable, setState, setTitle, writeObject

Methods inherited from class java.awt.Window

addOwnedWindow, addWindowListener, adjustListeningChildren, applyResourceBundle, applyResourceBundle, connectOwnedWindow, dispatchEventImpl, dispose, eventEnabled, getFocusOwner, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getOwnedWindows, getOwner, getToolkit, getWarningString, hide, isActive, isShowing, nextFocus, ownedInit, pack, postEvent, postWindowEvent, preProcessKeyEvent, processEvent, processWindowEvent, removeOwnedWindow, removeWindowListener, resetGC, setCursor, setFocusOwner, setWarningString, show, toBack, toFront, transferFocus

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventToSelf, doLayout, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getMaximumSize, getMinimumSize, getMouseEventTarget, getPreferredSize, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, numListening, paint, paintComponents, paintHeavyweightComponents, postsOldMouseEvents, preferredSize, print, printComponents, printHeavyweightComponents, processContainerEvent, proxyEnableEvents, proxyRequestFocus, remove, remove, removeAll, removeContainerListener, setFont, setLayout, update, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

strDataIsSortedFlag

boolean strDataIsSortedFlag

set once it is sorted

guesserTitle

static final java.lang.String guesserTitle

title for window

DEF_GNMID_TA_ROWS

static final int DEF_GNMID_TA_ROWS

default size of text area

DEF_GNMID_TA_COLS

static final int DEF_GNMID_TA_COLS

default size of text area

masterIDListSize

static int masterIDListSize

unsorted list of clone_id size

geneNameListSize

static int geneNameListSize

unsorted list of geneName size

geneNameList

static java.lang.String[] geneNameList

unsorted list of geneName, is G.C.'ed

masterIDList

static java.lang.String[] masterIDList

unsorted list of clone_id, is G.C.'ed

sortedGeneNameListStr

static java.lang.String sortedGeneNameListStr

sorted list of geneName

sortedClassIDListStr

static java.lang.String sortedClassIDListStr

sorted list of clone_id

taRows

int taRows

default size of text area

taCols

int taCols

default size of text area

doubleListFlag

boolean doubleListFlag

numeric/alpha or alpha only

Constructor Detail

PopupGeneGuesser

PopupGeneGuesser(MAExplorer maE,
                 char chFirstTyped,
                 java.awt.Font font)

PopupGeneGuesser() - constructor

Parameters:

maE - is instance of MAExplorer

chFirstTyped - is guesser character if not null

font - to use in text area

See Also:

Guesser.buildAndRunGuesser(java.lang.String), Guesser.setData(char, java.lang.String, java.lang.String[], int, int, int, java.lang.String, java.awt.Font), sortGeneNameAndCloneIDLists(MAExplorer)

Method Detail

sortGeneNameAndCloneIDLists

static void sortGeneNameAndCloneIDLists(MAExplorer mae)

sortGeneNameAndCloneIDLists() - sort lists of Master_IDs & Gene_Names for use with the guesser. This is ONCE-ONLY code.

Parameters:

mae - is instance of MAExplorer

See Also:

preSortLists(MAExplorer)

preSortLists

private static void preSortLists(MAExplorer mae)

preSortLists() - presort lists of Gene_Name and Master_ID for Guesser It copies the Gene data into the working geneNameList[] and the masterIDList[] with sizes geneNameListSize, masterIDListSize . It also removes the null entries and "Empty" entries.

Parameters:

mae - is instance of MAExplorer

See Also:

SortMAE.quickSortMultLists(java.lang.String[], java.lang.String[], int, int), SortMAE.uniqueInsert(java.lang.String[], java.lang.String[], int, java.lang.String, java.util.Hashtable), Util.cvtStrArrayToStr(java.lang.String[], int)

cancel

void cancel()

cancel() - cancel the guesser window

done

void done(java.lang.String resultStr)

done() - process the selected text, set current gene, and then popdown the guesser

Parameters:

resultStr - to set Current Gene if a single gene

See Also:

PopupRegistry.updateCurGeneInImageAndReg(java.lang.String)

setEGL

void setEGL(java.lang.String[] resultsList,
            java.lang.String resultStr)

setEGL() - process the selected text for setting EGL, popdown the guesser

Parameters:

resultsList - to set the EGL if saving a list

resultStr - to set Current Gene if a single gene

See Also:

EditedGeneList.setEGLfromGeneListStr(java.lang.String[])

clear

void clear()

clear() - clear the text field in the main window

updateAssocTextField

void updateAssocTextField(java.lang.String str)

updateAssocTextField() - update the associated text field

Overrides:

updateAssocTextField in class Guesser

Parameters:

str - is string to update the associated text field

updateAssocTextFieldCaretPos

void updateAssocTextFieldCaretPos(int pos)

updateAssocTextFieldCaretPos() - update assoc text field caret position

Overrides:

updateAssocTextFieldCaretPos in class Guesser

Parameters:

pos - is associated text field caret position