Class StateScrollers

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

All Implemented Interfaces:

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

class StateScrollers

extends java.awt.Frame

implements java.awt.event.AdjustmentListener, java.awt.event.ActionListener, java.awt.event.WindowListener, java.awt.event.MouseListener

The class builds a popup window dynamic grid of threshold parameter scrollers. This constitutes a set of state scrollers popup "control panel". Scrollers are associated with data filters which use the threshold. If a filter becomes active or inactive, then the scroller panel is regenerated and the panel will added or dropped to reflect the changes. The regenerated is invoked by EventMenu when the data filter is enabled or disabled.

There is no DONE button handler since users do not kill the window, but rather when it is killed when the associated Filter is disabled.

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: 2003/03/03 16:15:19 $ $Revision: 1.16 $

Author:

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

See Also:

MAExplorer Home, EventMenu, Filter, 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) java.awt.Button	adjustAllButton pop down current mode and popup adjust all sliders
(package private) boolean	allowPopdownOnWindowClosing Flag: allow popdown if orig.
(package private) java.awt.Button	applyButton Apply the parameters to the data filters.
(package private) java.awt.Color	bgColor optional background color ...
private Config	cfg link to global Config instance
private int	DEFAULT_PANEL_HEIGHT default height size of state scroller panel
private int	DEFAULT_PANEL_WIDTH default width size of state scroller panel
(package private) java.awt.Button	doneButton pop down (hide) the box - only in adjust all scrollers mode.
(package private) boolean	doRepaint
private int	gridCol size of grid for panel
private int	GRIDCOL size of grid for panel
private int	gridRow size of grid for panel
(package private) static int	idxClusterDist index for clusterDist threshold for cluster distance clustering
(package private) static int	idxCR1 index for CR1 Cy(3/5) ratio value lower bound
(package private) static int	idxCR2 index for CR2 Cy(3/5) ratio value upper bound
(package private) static int	idxCZ1 index for CZ1 Cy(3/5) zscore value lower bound
(package private) static int	idxCZ2 index for CZ2 Cy(3/5) zscore value upper bound
(package private) static int	idxdetValueSpotThr index for continuous threshold of Spot Detection values
(package private) static int	idxDiffXY index for Diff(HP-X,HP-Y) intensity differerence threshold
(package private) static int	idxNbrClusters index for # of clusters threshold for K-means clustering
(package private) static int	idxPctOK index for Percent SI OK (SI AT_LEAST/AT_MOST) QualCheck threshold
(package private) static int	idxPvalue index for p-value threshold value
(package private) static int	idxQualThr index for qualType continuous threshold of QualCheck values
(package private) static int	idxR1 index for R1 ratio HP-X/HP-Y value lower bound
(package private) static int	idxR2 index for R2 ratio HP-X/HP-Y value upper bound
(package private) static int	idxRadius index for Radius for drawing spots in the pseudo array
(package private) static int	idxSI1 index for Spot SI1 intensity value lower bound
(package private) static int	idxSI2 index for Spot SI2 intensity value upper bound
(package private) static int	idxSpot_CV index for spot Coefficient of Variation threshold value
(package private) static int	idxT1 index for I1 (T1) HP intensity value lower bound
(package private) static int	idxT2 index for I2 (T2) HP intensity value upper bound
(package private) static int	idxZ1 index for Z1 zscore value of (HP-X - HP-Y) lower bound
(package private) static int	idxZ2 index for Z2 zscore value of (HP-X - HP-Y) upper bound
(package private) boolean	isVisible Flag: if StateScroller GUI is visible
(package private) java.awt.Panel	lowerControlPanel holds buttons, textAreas, etc for state scroller GUI
private MAExplorer	mae link to global MAExplorer instance
(package private) java.awt.TextArea	mouseoverTA mouseover TextArea
(package private) java.awt.Font	newFontLbl font type for labels
(package private) static int	nSB # of entries in sbName[] tables
(package private) java.awt.Panel	pgrid holds the Scrollbar (SB) panels
private int	pnlHeight panel size height
private int	pnlWidth panel size Width
private int	PREFERRED_PANEL_HEIGHT max width size of state scroller panel
private int	PREFERRED_PANEL_WIDTH max height size of state scroller panel
(package private) boolean	runClusterAnalysis
(package private) boolean	runFilter
(package private) boolean	runImageOptimizer
(package private) boolean	runKmeansClusterAnalysis
(package private) boolean[]	sbActive Flags: true if scroll bars are active
(package private) java.awt.Scrollbar[]	sbBar list of scroll bars
(package private) float[]	sbCurValue current & initial (STATE) values of scrollbar
(package private) int[]	sbGTidx corresponding GT scroller integer bounds
(package private) java.awt.Label[]	sbLblName label of Name to left of scrollbar
(package private) java.awt.Label[]	sbLblValue label of Values to right of scrollbar
(package private) float[]	sbLowerBound Note: lower bounds in STATE space
(package private) int[]	sbLTidx corresponding LT scroller integer bounds
(package private) static java.lang.String[]	sbMouseMsg messages for mouseover of label
(package private) static java.lang.String[]	sbName list of state scroller label names
(package private) boolean[]	sbNonLinearScale Flags for using a nonlinear vernier in the SCROLLER CONTROLs
(package private) int[]	sbPrecision # of digits in scroller value labels
(package private) int[]	sbSize size of scale in Scroller space
(package private) float[]	sbUpperBound Note: upper bounds in STATE space
private java.awt.Point	scrPos Normal position for showing selected state.
(package private) static int	TA_COLS size of mouseover TextArea
(package private) static int	TA_ROWS size of mouseover TextArea
(package private) java.lang.String	title holds title string for state scroller GUI
(package private) java.awt.Label	titleLabel Label for title
(package private) boolean	useAllScrollersFlag Flag: force all scrollers to appear even if not used...
(package private) int[]	useFilterCounters # of filters dependent on each slider.
private Util	util link to global Util instance

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, font, 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)

StateScrollers(MAExplorer mae, java.lang.String title) StateScrollers() - constructor to build the GUI with pop up menus

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle button clicks
(package private) boolean	addScroller(java.lang.String scrollBarName) addScroller() - add a particular scroller by scroller name
void	adjustmentValueChanged(java.awt.event.AdjustmentEvent e) adjustmentValueChanged() - handle scroller state changed events
(package private) void	adjustRatioOrZscoreCounters() adjustRatioOrZscoreCounters() - adjust any sliders that depend on being in Zscore mode This is ONLY called when mae.isZscoreFlag is changed.
(package private) void	clearActiveScrollers() clearActiveScrollers() - clear list of all active scrollers
(package private) void	clearPostProcessingFlags() clearPostProcessingFlags() - clear special post-processing flags that are then set by particular scroller changes
(package private) void	createStateScrollers() createStateScrollers() - build the grid panel of popup scrollers
(package private) int	cvRatioToScrollValue(float rValF) cvRatioToScrollValue() - convert state ratio to ratio-scroller value
(package private) float	cvScrollToStateValue(int idx, int sbVal) cvScrollToStateValue() - cvt scrollbar value to (float) STATE value
(package private) double	cvScrollValueToRatio(int val, int size) cvScrollValueToRatio() - convert ratio-scroller value to ratio STATE value
(package private) int	cvStateToScrollValue(int idx, float stVal) cvStateToScrollValue() - convert STATE value to scrollbar current value.
java.awt.Dimension	getPreferredSize_DEPRICATED() getPreferredSize() - get the preferred size
private void	initPreloads() initPreloads() - setup the preloaded arrays of filter names, values and range gang-scroll option.
(package private) void	initUserFilterScrollerCounters() initUserFilterScrollerCounters() - initialize scroller use counters based on the State flags.
(package private) int	lookupScrollerIdx(java.lang.String scrollBarName) lookupScrollerIdx() - lookup a particular scroller index
void	mouseClicked(java.awt.event.MouseEvent me)
void	mouseEntered(java.awt.event.MouseEvent me) mouseEntered() - put mouse over data in MouseOver text area
void	mouseExited(java.awt.event.MouseEvent me) mouseExited() - clear mouseover text area.
void	mouseMoved(java.awt.event.MouseEvent me)
void	mousePressed(java.awt.event.MouseEvent me)
void	mouseReleased(java.awt.event.MouseEvent me)
(package private) int	nbrActiveScrollers() nbrActiveScrollers() - return the number of active scrollers and copy scaled scroller data to the state variables.
(package private) int	nbrActiveScrollersUseCounters() nbrActiveScrollersUseCounters() - return the number of active scrollers and copy scaled scroller data to the state variables.
(package private) void	popdownScrollers() popdownScrollers() - close down the window using dispose
(package private) void	regenerateScrollers(boolean popupAllScrollersFlag) regenerateScrollers() - regenerate scroller window
(package private) boolean	reRunClusterAnalysis() reRunClusterAnalysis() - rerun cluster analysis after changed state.
(package private) boolean	reRunImageOptimizer() reRunImageOptimizer() - rerun pseudoarray image optimization after changed state.
(package private) boolean	rmvScroller(java.lang.String scrollBarName) rmvScroller() - remove a particular scroller by scroller name
(package private) void	setEnablePopupScrollbars(boolean showIt) setEnablePopupScrollbars() - hide or show popup all scrollbars
(package private) void	setRangeMaps() setRangeMaps() - set norm dependent scrollers based normalization method.
(package private) void	setRangeMapsFromState() setRangeMapsFromState() - set normalization dependent scrollers based on norm.
(package private) boolean	setThresholdValueBySliderIdx(int idx, float value) setThresholdValueBySliderIdx() - set slider threshold value by slider index
(package private) boolean	setUseAllScrollersFlag(boolean newFlag) setUseAllScrollersFlag() - set the state to display all scrollers by flag.
(package private) boolean	updateFilterScrollerUseCounter(java.lang.String scrollBarName, boolean addFlag) updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller name.
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - close the window - don't allow unless doing ALL scrollers.
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 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

mae

private MAExplorer mae

link to global MAExplorer instance

cfg

private Config cfg

link to global Config instance

util

private Util util

link to global Util instance

TA_ROWS

static final int TA_ROWS

size of mouseover TextArea

TA_COLS

static final int TA_COLS

size of mouseover TextArea

DEFAULT_PANEL_WIDTH

private final int DEFAULT_PANEL_WIDTH

default width size of state scroller panel

DEFAULT_PANEL_HEIGHT

private final int DEFAULT_PANEL_HEIGHT

default height size of state scroller panel

PREFERRED_PANEL_HEIGHT

private final int PREFERRED_PANEL_HEIGHT

max width size of state scroller panel

PREFERRED_PANEL_WIDTH

private final int PREFERRED_PANEL_WIDTH

max height size of state scroller panel

GRIDCOL

private final int GRIDCOL

size of grid for panel

scrPos

private java.awt.Point scrPos

Normal position for showing selected state. If showing all states, then move Vert position to near top

sbName

static java.lang.String[] sbName

list of state scroller label names

nSB

static final int nSB

# of entries in sbName[] tables

sbMouseMsg

static java.lang.String[] sbMouseMsg

messages for mouseover of label

idxSI1

static final int idxSI1

index for Spot SI1 intensity value lower bound

idxSI2

static final int idxSI2

index for Spot SI2 intensity value upper bound

idxT1

static final int idxT1

index for I1 (T1) HP intensity value lower bound

idxT2

static final int idxT2

index for I2 (T2) HP intensity value upper bound

idxR1

static final int idxR1

index for R1 ratio HP-X/HP-Y value lower bound

idxR2

static final int idxR2

index for R2 ratio HP-X/HP-Y value upper bound

idxZ1

static final int idxZ1

index for Z1 zscore value of (HP-X - HP-Y) lower bound

idxZ2

static final int idxZ2

index for Z2 zscore value of (HP-X - HP-Y) upper bound

idxCR1

static final int idxCR1

index for CR1 Cy(3/5) ratio value lower bound

idxCR2

static final int idxCR2

index for CR2 Cy(3/5) ratio value upper bound

idxCZ1

static final int idxCZ1

index for CZ1 Cy(3/5) zscore value lower bound

idxCZ2

static final int idxCZ2

index for CZ2 Cy(3/5) zscore value upper bound

idxPvalue

static final int idxPvalue

index for p-value threshold value

idxSpot_CV

static final int idxSpot_CV

index for spot Coefficient of Variation threshold value

idxRadius

static final int idxRadius

index for Radius for drawing spots in the pseudo array

idxClusterDist

static final int idxClusterDist

index for clusterDist threshold for cluster distance clustering

idxNbrClusters

static final int idxNbrClusters

index for # of clusters threshold for K-means clustering

idxDiffXY

static final int idxDiffXY

index for Diff(HP-X,HP-Y) intensity differerence threshold

idxPctOK

static final int idxPctOK

index for Percent SI OK (SI AT_LEAST/AT_MOST) QualCheck threshold

idxQualThr

static final int idxQualThr

index for qualType continuous threshold of QualCheck values

idxdetValueSpotThr

static final int idxdetValueSpotThr

index for continuous threshold of Spot Detection values

allowPopdownOnWindowClosing

boolean allowPopdownOnWindowClosing

Flag: allow popdown if orig. window closing

doRepaint

boolean doRepaint

runImageOptimizer

boolean runImageOptimizer

runClusterAnalysis

boolean runClusterAnalysis

runKmeansClusterAnalysis

boolean runKmeansClusterAnalysis

runFilter

boolean runFilter

sbSize

int[] sbSize

size of scale in Scroller space

sbUpperBound

float[] sbUpperBound

Note: upper bounds in STATE space

sbLowerBound

float[] sbLowerBound

Note: lower bounds in STATE space

sbCurValue

float[] sbCurValue

current & initial (STATE) values of scrollbar

sbLTidx

int[] sbLTidx

corresponding LT scroller integer bounds

sbGTidx

int[] sbGTidx

corresponding GT scroller integer bounds

sbPrecision

int[] sbPrecision

# of digits in scroller value labels

sbNonLinearScale

boolean[] sbNonLinearScale

Flags for using a nonlinear vernier in the SCROLLER CONTROLs

useFilterCounters

int[] useFilterCounters

# of filters dependent on each slider. Each filter that requires that slider will increment the counter when it is enabled and decrement the counter when it is disabled.

title

java.lang.String title

holds title string for state scroller GUI

lowerControlPanel

java.awt.Panel lowerControlPanel

holds buttons, textAreas, etc for state scroller GUI

doneButton

java.awt.Button doneButton

pop down (hide) the box - only in adjust all scrollers mode. Normally, can only pop it down if there are NO associated data Filters.

applyButton

java.awt.Button applyButton

Apply the parameters to the data filters. Only in adjust all scrollers mode. Normally, automatically apply it by calling the data filters if not adjusting all scrollers mode.

adjustAllButton

java.awt.Button adjustAllButton

pop down current mode and popup adjust all sliders

mouseoverTA

java.awt.TextArea mouseoverTA

mouseover TextArea

titleLabel

java.awt.Label titleLabel

Label for title

sbLblName

java.awt.Label[] sbLblName

label of Name to left of scrollbar

sbLblValue

java.awt.Label[] sbLblValue

label of Values to right of scrollbar

sbBar

java.awt.Scrollbar[] sbBar

list of scroll bars

sbActive

boolean[] sbActive

Flags: true if scroll bars are active

pgrid

java.awt.Panel pgrid

holds the Scrollbar (SB) panels

bgColor

java.awt.Color bgColor

optional background color ...

newFontLbl

java.awt.Font newFontLbl

font type for labels

useAllScrollersFlag

boolean useAllScrollersFlag

Flag: force all scrollers to appear even if not used...

isVisible

boolean isVisible

Flag: if StateScroller GUI is visible

pnlWidth

private int pnlWidth

panel size Width

pnlHeight

private int pnlHeight

panel size height

gridCol

private int gridCol

size of grid for panel

gridRow

private int gridRow

size of grid for panel

Constructor Detail

StateScrollers

StateScrollers(MAExplorer mae,
               java.lang.String title)

StateScrollers() - constructor to build the GUI with pop up menus

Parameters:

mae - is MAExplorer instance

title - is the title for the state scroller popup window

See Also:

initPreloads()

Method Detail

getPreferredSize_DEPRICATED

public java.awt.Dimension getPreferredSize_DEPRICATED()

getPreferredSize() - get the preferred size

Returns:

window size

initPreloads

private void initPreloads()

initPreloads() - setup the preloaded arrays of filter names, values and range gang-scroll option. [TODO] Note: the ranges may be gotten from the .mae state file. In particular, the following are normalization and state dependent: sbUpperBound[], sbLowerBound[], sbCurValue[] The solution is to save these bounds in the state as well (what a pain!) or to recalculate them (also a pain...).

See Also:

setRangeMaps()

setUseAllScrollersFlag

boolean setUseAllScrollersFlag(boolean newFlag)

setUseAllScrollersFlag() - set the state to display all scrollers by flag.

Parameters:

newFlag - is the value to set the all scrollers flag to.

Returns:

the previous value

createStateScrollers

void createStateScrollers()

createStateScrollers() - build the grid panel of popup scrollers

See Also:

Util.cvf2s(float, int), cvStateToScrollValue(int, float)

clearActiveScrollers

void clearActiveScrollers()

clearActiveScrollers() - clear list of all active scrollers

lookupScrollerIdx

int lookupScrollerIdx(java.lang.String scrollBarName)

lookupScrollerIdx() - lookup a particular scroller index

Parameters:

scrollBarName - is the name of the scroller to lookup by name

Returns:

-1 if failed, else an index >= 0 if successful;

addScroller

boolean addScroller(java.lang.String scrollBarName)

addScroller() - add a particular scroller by scroller name

Parameters:

scrollBarName - is the name of the scroller to add by name

Returns:

true if successful;

rmvScroller

boolean rmvScroller(java.lang.String scrollBarName)

rmvScroller() - remove a particular scroller by scroller name

Parameters:

scrollBarName - is the name of the scroller to remove by name

Returns:

true if successful

updateFilterScrollerUseCounter

boolean updateFilterScrollerUseCounter(java.lang.String scrollBarName,
                                       boolean addFlag)

updateFilterScrollerUseCounter() - "add" or "remove" use of a particular scroller by scroller name. This method is called both by the EventMenu handlers when the Filter flags change and by plugins via the MJA.

Parameters:

scrollBarName - is the name of the scroller to update by name in sbName[0:nSB-1]

addFlag - to add a counter if true else remove a counter if false

Returns:

true if successful

adjustRatioOrZscoreCounters

void adjustRatioOrZscoreCounters()

adjustRatioOrZscoreCounters() - adjust any sliders that depend on being in Zscore mode This is ONLY called when mae.isZscoreFlag is changed. This is called if Zscore mode is CHANGED while ratio mode is still active.

initUserFilterScrollerCounters

void initUserFilterScrollerCounters()

initUserFilterScrollerCounters() - initialize scroller use counters based on the State flags.

 1. called from EventMenu handlers when change the flags
 2. plugins will modify counters separately through other calls.

setEnablePopupScrollbars

void setEnablePopupScrollbars(boolean showIt)

setEnablePopupScrollbars() - hide or show popup all scrollbars

Parameters:

showIt - flag to hide or show popup state scrollers

cvScrollToStateValue

float cvScrollToStateValue(int idx,
                           int sbVal)

cvScrollToStateValue() - cvt scrollbar value to (float) STATE value

 If using a log scale, then
        stVal = alpha*(sbValue**2)+beta,
 where: alpha = (ub-lb)/(sbSize**2-1),
        beta  = ( (ub+lb)-alpha*(sbSize**2+1) )/2.

Parameters:

idx - is the index of the scroller to convert

sbVal - is the scroller space value of the scroller to convert

Returns:

value in state space

See Also:

cvScrollValueToRatio(int, int)

cvStateToScrollValue

int cvStateToScrollValue(int idx,
                         float stVal)

cvStateToScrollValue() - convert STATE value to scrollbar current value.

 If using a log scale, then
      ubMlbRange= (ub-lb),
      stMlbVal= (sbMax -stVal -lb),
      r= (stMlbVal / ubMlbRange),
      rLog= r*log(sbMax+1.0),
      sbVal= sbMax - (exp(rLog) - 1.0).

Parameters:

idx - is the index of the scroller to convert

stVal - is the space space value of the scroller to convert

Returns:

value in scroller space

See Also:

cvRatioToScrollValue(float)

cvRatioToScrollValue

int cvRatioToScrollValue(float rValF)

cvRatioToScrollValue() - convert state ratio to ratio-scroller value

Parameters:

rValF - is the ratio scroller value

Returns:

value

cvScrollValueToRatio

double cvScrollValueToRatio(int val,
                            int size)

cvScrollValueToRatio() - convert ratio-scroller value to ratio STATE value

Parameters:

val - is the ratio scroller value

size - is the max size of the val range.

Returns:

value

clearPostProcessingFlags

void clearPostProcessingFlags()

clearPostProcessingFlags() - clear special post-processing flags that are then set by particular scroller changes

reRunImageOptimizer

boolean reRunImageOptimizer()

reRunImageOptimizer() - rerun pseudoarray image optimization after changed state. If it succeeds, the caller needs to do a global repaint.

Returns:

true if succeed, in which case the caller needs to repaint.

reRunClusterAnalysis

boolean reRunClusterAnalysis()

reRunClusterAnalysis() - rerun cluster analysis after changed state. If it succeeds, the caller needs to do a global repaint.

Returns:

true if succeed, in which case the caller needs to repaint.

See Also:

ClusterGenes, ClusterGenes.updateKmeansClusters(), PopupRegistry.updateCurGene(int, int, java.lang.Object)

adjustmentValueChanged

public void adjustmentValueChanged(java.awt.event.AdjustmentEvent e)

adjustmentValueChanged() - handle scroller state changed events

Specified by:

adjustmentValueChanged in interface java.awt.event.AdjustmentListener

See Also:

Filter.computeWorkingGeneList(), Component.repaint(), Util.cvf2s(float, int), clearPostProcessingFlags(), cvScrollToStateValue(int, int), cvStateToScrollValue(int, float), reRunImageOptimizer(), reRunClusterAnalysis(), setThresholdValueBySliderIdx(int, float)

setThresholdValueBySliderIdx

boolean setThresholdValueBySliderIdx(int idx,
                                     float value)

setThresholdValueBySliderIdx() - set slider threshold value by slider index

Parameters:

idx - is the index of the slider value in the sbName[]

Returns:

false if invalid index, true if valid index. Need to check additional flags that may be set here.
Side effects: one or more flags may be set including: runFilter, runImageOptimizer, runClusterAnalysis, runKmeansClusterAnalysis
Note the flags should be cleared BEFORE calling this method.

See Also:

clearPostProcessingFlags()

actionPerformed

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

actionPerformed() - Handle button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

See Also:

clearActiveScrollers(), popdownScrollers()

popdownScrollers

void popdownScrollers()

popdownScrollers() - close down the window using dispose

nbrActiveScrollers

int nbrActiveScrollers()

nbrActiveScrollers() - return the number of active scrollers and copy scaled scroller data to the state variables.

Returns:

# of active scrollers

nbrActiveScrollersUseCounters

int nbrActiveScrollersUseCounters()

nbrActiveScrollersUseCounters() - return the number of active scrollers and copy scaled scroller data to the state variables. This is based on the user counters being > 0.

Returns:

# of active scrollers

regenerateScrollers

void regenerateScrollers(boolean popupAllScrollersFlag)

regenerateScrollers() - regenerate scroller window

Parameters:

popupAllScrollersFlag - will popup a window with ALL scrollers active

See Also:

addScroller(java.lang.String), clearActiveScrollers(), createStateScrollers(), nbrActiveScrollers(), popdownScrollers()

setRangeMaps

void setRangeMaps()

setRangeMaps() - set norm dependent scrollers based normalization method.

See Also:

setRangeMapsFromState()

setRangeMapsFromState

void setRangeMapsFromState()

setRangeMapsFromState() - set normalization dependent scrollers based on norm. method.

See Also:

MaHybridSample.scaleIntensData(float)

windowClosing

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

windowClosing() - close the window - don't allow unless doing ALL scrollers.

Specified by:

windowClosing in interface java.awt.event.WindowListener

See Also:

Util.cvf2s(float, int), Util.saveCmdHistory(java.lang.String), Util.showMsg1(java.lang.String, java.awt.Color, java.awt.Color), Util.showMsg2(java.lang.String), Util.showMsg3(java.lang.String), clearActiveScrollers(), popdownScrollers()

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

windowOpened

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

Specified by:

windowOpened in interface java.awt.event.WindowListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent me)

mouseEntered() - put mouse over data in MouseOver text area

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent me)

mouseExited() - clear mouseover text area.

Specified by:

mouseExited in interface java.awt.event.MouseListener

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent me)

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent me)

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mousePressed

public void mousePressed(java.awt.event.MouseEvent me)

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent me)

Specified by:

mouseReleased in interface java.awt.event.MouseListener