gov.lbl.genome.gui
Class VistaApp

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  javax.swing.JApplet
                      gov.lbl.genome.gui.VistaApp

All Implemented Interfaces:

java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.lang.Runnable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer

public class VistaApp
extends javax.swing.JApplet
implements java.lang.Runnable, java.awt.event.WindowListener

Title: VistaApp

Description: The entry point into the UI. This is a singleton classs.

Copyright: Copyright (c) 2002 Ernest Orlando Lawrence Berkeley National Laboratory

Company: LBNL

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JApplet.AccessibleJApplet

Nested classes/interfaces inherited from class java.applet.Applet

java.applet.Applet.AccessibleApplet

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

java.awt.Panel.AccessibleAWTPanel

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

boolean	canResize
boolean	cuready
static boolean	debugAction
static boolean	debugComm
static boolean	debugException
static boolean	debugInit
static boolean	debugProgress
GeneSearchPanel	geneSearchPanel
static java.awt.Image	legend
java.awt.print.PageFormat	pageFormat
java.awt.print.Paper	paper
java.awt.print.PrinterJob	printJob
static java.lang.String	RELEASE_DATE
Resource	resource This public parameter provides access to the default section of the resource file.
java.lang.String	scrollbar
boolean	started
boolean	useParameters

Fields inherited from class javax.swing.JApplet

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

VistaApp()
VistaApp is the main class of the applet

Method Summary

void	checkCurves(java.lang.String pos) Method checkCurves starts separate thread, check curves for visibility and set visibility rules for displayed curves
void	clearStatusBar() remove any text from the status bar
int	convertX(double X, int line, int offset, int width) convert chromosome coordinate into screen coordinate, according to the line number, offset and panel width
int	convertX(long X, int line, int offset, int width) convert chromosome coordinate into screen coordinate,
void	disableGUI() call setEnabled(false) for all components joined with action
void	enableGUI() call setEnabled(true) for all components joined with action
void	enablePrinting(boolean key) enable or disable printing actions The only reason of using this method is bug in java 1.5
void	freezeCounters(boolean f) Stop applet timer
javax.swing.AbstractAction	getAddAction() return addAction3
GenomeInfo	getBaseGenome() get baseGenome
java.lang.String	getBG() return base genome name
int	getCalcWindow() return calc.
java.lang.String	getChrom() return current chromosome
java.lang.String	getChrom(java.lang.String posString) try to extract chromosome name from the position string
long	getChromSize() return size of current chromosome or contig
long	getChromSize(java.lang.String chr) Return chromosome size.
CommUnit	getCommUnit() return a CommUnit object
java.net.HttpURLConnection	getConnection() return connection field
int	getConsIdentity() return cons.
int	getConsWidth() return minConsWidth
int	getDataInterval() return interval between two pixils
java.lang.String	getDefaultGenes() getDefaultGenes
javax.swing.AbstractAction	getDetailsAction() return detailsAction2
Element	getDialogElement(java.lang.String name) Retern Element from XML Document from dialogs.xml
DisplayPanel	getDisplayPanel() getDisplayPanel
ErrorHandler	getErrorHandler() return handler of the Error Message Box
GenesInfo[]	getGenesInfo() getGenesInfo
int	getGraphWidth() return adjusted width of a curve panel
History	getHistory() Return history object
java.awt.Image	getImage(java.lang.String name) download image from the server
java.io.InputStream	getInputStream() return InputStream from the connection
long	getMaxX() return maxX
long	getMaxX(int i) return maxX for "i" line
long	getMaxX(java.lang.String posString) try to extract maxX from the position string
int	getMaxY() deturn default/actual maxY value
int	getMaxY(CurveInfo curve) rerurn maxY parameter for the curve.
long	getMinX() return minX
long	getMinX(int i) return minX for "i" line
long	getMinX(java.lang.String posString) try to extract minX from the position string
int	getMinY() deturn default/actual minY value
int	getMinY(CurveInfo curve) rerurn minY parameter for the curve.
int	getNewHeight() return newHeight
int	getNewWidth() return newWidth
int	getNumDataPoints() return expected number of data points.
java.io.OutputStream	getOutputStream(java.lang.String type) return OutputStream to "POST" data to the server ToDo This method should throw an exception instead of returning something
int	getParam(java.lang.String parName, int defValue) try to get integer from Map parameters, then from applet getParameter(String) or return default value
java.lang.String	getParam(java.lang.String parName, java.lang.String defValue) try to get String from Map parameters, then from applet getParameter(String) or return default value
java.lang.String	getPos() return position as formated string
java.lang.String	getPositionString() return formated position string
java.lang.String	getPostHeader() getPostHeader
static java.lang.String	getRandomString(int length) return string of specified length with rndom content
javax.swing.AbstractAction	getRemoveAction() return removeAction2
java.lang.String	getRuns() return servlet-ready formated run list.
java.lang.String	getSelectedOrg() get selected organism
javax.swing.AbstractAction	getSettingsAction() return settingsAction2
java.lang.String	getShow() return a servlet parameter "showdefaults"
javax.swing.AbstractAction	getStatAction() return statAction2
SwapCurvesAction	getSwapCurvesAction()
java.lang.String	getTextbrowserURL() return URL for the text browser
java.lang.String	getVersion() getVersion
void	init() This is an important and big method.
boolean	isChrom() return true if current contig is real chromosome
boolean	isDangerous() return true if action can destroy the applet.
boolean	isDefaultVisible() show or not to show default curves
boolean	isIdle1() return true if idle more than 20 min
boolean	isIdle2() return true if idle more than 30 sec
boolean	isIdle3() return true if idle more than 0.5 sec
boolean	isReady()
void	lastPosition() set status from previous position
void	nextPosition() set status from nextPosition
void	printStatusBar(java.lang.String s) show sring in the status bar
void	pushInHistory() push curent status in history
void	refreshOrgList() refresh organism list in the pull-dawn menu
void	release() Do some work and refresh panels after slow operations, like data pulling
void	resetConnection() set connection to null
void	resetCounter1() start 20 min counter
void	resetCounter2() start 30 sec counter
void	resetCounter3() start 0.5 sec min counter
void	run() Main thread of the applet.
void	setBaseGenome(GenomeInfo baseGenome) set baseGenome
void	setChrom(java.lang.String chr) set current chromosome
void	setDangerous(boolean d) Some actions set dangerous field in true in order to disable other actions.
static void	setDebugLevel(java.lang.String dLevel) debugInit = "1" or "init" debugProgress = "2" or "progress" debugComm = "4" or "comm" debugAction = "8" or "action" debugException = "16" or "exception" debug All = 1|2|4|8|16 or "all"
void	setDetailsActionEnabled(boolean flag) call setEnabled(boolean) for detailsAction and detailsAction2
void	setForwardBackBtns() Enable od disable >> or/ond << button
void	setNewHeight(int nh) setNewHeight
boolean	setNewSize(int width, int height) This method is called from JavaScript and sets new applet size.
void	setNewWidth(int nw) setNewWidth
void	setOrgLabel(int org) set orgLabel
void	setParam(java.lang.String param, java.lang.Object val) replace an object in the parameters Map
void	setPositionString(java.lang.String string) set position (chromosome, start, end) from formated string
void	setPositionString(java.lang.String chr, java.lang.String min, java.lang.String max) set position from parameters
void	setReady(boolean f)
void	setSettingsVisible(boolean b) Enable or disable settings actions
void	setUCSCActionTip(java.lang.String tip) Set ToolTip for UCSC action button and menu.
void	startProgress(java.lang.String desc) Start RIGHT-TOP DNA Icon rotation set ready(false), stop timers, disable GUI, write comment in the status bar
void	stopProgress() Stop RIGHT-TOP DNA Icon rotation start timers, enable GUI, remove comment from the status bar
void	swapCurves() Switch base genome.
void	testPosition(int minx, int maxx) testPosition
void	upDate() currently Not used Check server for new and deleted curves and new versions since start time.
void	updateContig(java.lang.String s)
void	updateCurrPosition(java.lang.String s)
boolean	updatePosition() updatePosition is a key method for geting curves.
boolean	updatePosition(long minX, long maxX) updatePosition is a key method for geting curves.
boolean	updatePosition(java.lang.String position) updatePosition is a key method for geting curves.
boolean	updatePosition(java.lang.String chrom, long minX, long maxX) updatePosition is a key method for geting curves.
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) Stop dataPuller thread when closing
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.JApplet

addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isRootPaneCheckingEnabled, paramString, remove, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.applet.Applet

destroy, getAppletContext, getAppletInfo, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus, start, stop

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, 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, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

resource

public Resource resource

This public parameter provides access to the default section of the resource file.

RELEASE_DATE

public static final java.lang.String RELEASE_DATE

See Also:

Constant Field Values

debugInit

public static boolean debugInit

debugComm

public static boolean debugComm

debugProgress

public static boolean debugProgress

debugAction

public static boolean debugAction

cuready

public boolean cuready

started

public boolean started

canResize

public boolean canResize

useParameters

public boolean useParameters

geneSearchPanel

public GeneSearchPanel geneSearchPanel

legend

public static java.awt.Image legend

printJob

public java.awt.print.PrinterJob printJob

pageFormat

public java.awt.print.PageFormat pageFormat

paper

public java.awt.print.Paper paper

scrollbar

public java.lang.String scrollbar

debugException

public static boolean debugException

Constructor Detail

VistaApp

public VistaApp()

VistaApp is the main class of the applet

Method Detail

getCommUnit

public CommUnit getCommUnit()

return a CommUnit object

Returns:

CommUnit

getErrorHandler

public ErrorHandler getErrorHandler()

return handler of the Error Message Box

Returns:

ErrorHandler

updatePosition

public boolean updatePosition()

updatePosition is a key method for geting curves.

Returns:

boolean

See Also:

updatePosition(String,long,long)

updatePosition

public boolean updatePosition(long minX,
                              long maxX)

updatePosition is a key method for geting curves.

Parameters:

minX - long

maxX - long

Returns:

boolean

See Also:

updatePosition(String,long,long)

getChrom

public java.lang.String getChrom(java.lang.String posString)
                          throws java.lang.Exception

try to extract chromosome name from the position string

Parameters:

posString - String

Returns:

long

Throws:

java.lang.Exception

getMinX

public long getMinX(java.lang.String posString)
             throws java.lang.Exception

try to extract minX from the position string

Parameters:

posString - String

Returns:

long

Throws:

java.lang.Exception

getMaxX

public long getMaxX(java.lang.String posString)
             throws java.lang.Exception

try to extract maxX from the position string

Parameters:

posString - String

Returns:

long

Throws:

java.lang.Exception

updatePosition

public boolean updatePosition(java.lang.String position)

updatePosition is a key method for geting curves.

Parameters:

position - String

Returns:

boolean

See Also:

updatePosition(String,long,long)

updatePosition

public boolean updatePosition(java.lang.String chrom,
                              long minX,
                              long maxX)

updatePosition is a key method for geting curves.

Parameters:

chrom - String

minX - long

maxX - long

Returns:

boolean

isChrom

public boolean isChrom()

return true if current contig is real chromosome

Returns:

boolean

getPositionString

public java.lang.String getPositionString()

return formated position string

Returns:

String

setPositionString

public void setPositionString(java.lang.String chr,
                              java.lang.String min,
                              java.lang.String max)
                       throws java.lang.Exception

set position from parameters

Parameters:

chr - String

min - String

max - String

Throws:

java.lang.Exception

See Also:

setPositionString(String)

setPositionString

public void setPositionString(java.lang.String string)
                       throws java.lang.Exception

set position (chromosome, start, end) from formated string

Parameters:

string - String

Throws:

java.lang.Exception

See Also:

setPositionString(String,String,String)

lastPosition

public void lastPosition()

set status from previous position

nextPosition

public void nextPosition()

set status from nextPosition

pushInHistory

public void pushInHistory()

push curent status in history

setForwardBackBtns

public void setForwardBackBtns()

Enable od disable >> or/ond << button

getBaseGenome

public GenomeInfo getBaseGenome()

get baseGenome

Returns:

GenomeInfo

getSelectedOrg

public java.lang.String getSelectedOrg()

get selected organism

Returns:

String

See Also:

BaseInfoPanel.getSelectedOrg()

setOrgLabel

public void setOrgLabel(int org)

set orgLabel

Parameters:

org - int

See Also:

BaseInfoPanel.setOrgLabel(int)

setBaseGenome

public void setBaseGenome(GenomeInfo baseGenome)

set baseGenome

Parameters:

baseGenome - GenomeInfo

getMinX

public long getMinX()

return minX

Returns:

long

See Also:

getMaxX(int), getMinX(int), getMaxX()

getMaxX

public long getMaxX()

return maxX

Returns:

long

See Also:

getMaxX(int), getMinX(int), getMinX()

getMinX

public long getMinX(int i)

return minX for "i" line

Parameters:

i - int

Returns:

long

See Also:

getMaxX(), getMaxX(int), getMinX()

getMaxX

public long getMaxX(int i)

return maxX for "i" line

Parameters:

i - int

Returns:

long

See Also:

getMaxX(), getMinX(int), getMinX()

getConsIdentity

public int getConsIdentity()

return cons. identity (parameter "min_id")

Returns:

int

getCalcWindow

public int getCalcWindow()

return calc. window (parameter "window")

Returns:

int

getMinY

public int getMinY()

deturn default/actual minY value

Returns:

int

See Also:

getMaxY(CurveInfo), getMaxY()

getMinY

public int getMinY(CurveInfo curve)

rerurn minY parameter for the curve. This parameter determins minY of the curve at startup.

Parameters:

curve - CurveInfo

Returns:

int

See Also:

getMaxY(CurveInfo), getMaxY()

getMaxY

public int getMaxY()

deturn default/actual maxY value

Returns:

int

See Also:

getMinY(CurveInfo), getMinY()

getMaxY

public int getMaxY(CurveInfo curve)

rerurn maxY parameter for the curve. This parameter determins maxY of the curve at startup.

Parameters:

curve - CurveInfo

Returns:

int

See Also:

getMinY(CurveInfo), getMinY()

getConsWidth

public int getConsWidth()

return minConsWidth

Returns:

int

isDefaultVisible

public boolean isDefaultVisible()

show or not to show default curves

Returns:

boolean

setChrom

public void setChrom(java.lang.String chr)

set current chromosome

Parameters:

chr - String

getChrom

public java.lang.String getChrom()

return current chromosome

Returns:

String

getConnection

public java.net.HttpURLConnection getConnection()

return connection field

Returns:

HttpURLConnection

getInputStream

public java.io.InputStream getInputStream()

return InputStream from the connection

Returns:

InputStream

resetConnection

public void resetConnection()

set connection to null

getGenesInfo

public GenesInfo[] getGenesInfo()

getGenesInfo

Returns:

GenesInfo[]

See Also:

GenesInfo, GenomeInfo.getGenesInfos()

getDefaultGenes

public java.lang.String getDefaultGenes()

getDefaultGenes

Returns:

String

getOutputStream

public java.io.OutputStream getOutputStream(java.lang.String type)

return OutputStream to "POST" data to the server ToDo This method should throw an exception instead of returning something

Parameters:

type - String

Returns:

OutputStream

getImage

public java.awt.Image getImage(java.lang.String name)

download image from the server

Parameters:

name - String

Returns:

Image

getTextbrowserURL

public java.lang.String getTextbrowserURL()

return URL for the text browser

Returns:

String

getRuns

public java.lang.String getRuns()

return servlet-ready formated run list.

Returns:

String

getPos

public java.lang.String getPos()

return position as formated string

Returns:

String

getShow

public java.lang.String getShow()

return a servlet parameter "showdefaults"

Returns:

String

getBG

public java.lang.String getBG()

return base genome name

Returns:

String

printStatusBar

public void printStatusBar(java.lang.String s)

show sring in the status bar

Parameters:

s - String

clearStatusBar

public void clearStatusBar()

remove any text from the status bar

stopProgress

public void stopProgress()

Stop RIGHT-TOP DNA Icon rotation start timers, enable GUI, remove comment from the status bar

See Also:

startProgress(String)

startProgress

public void startProgress(java.lang.String desc)

Start RIGHT-TOP DNA Icon rotation set ready(false), stop timers, disable GUI, write comment in the status bar

Parameters:

desc - String #see stopProgress()

init

public void init()

This is an important and big method. A lot of parameters and objects are created here.

Overrides:

init in class java.applet.Applet

getDataInterval

public int getDataInterval()

return interval between two pixils

Returns:

int

getNumDataPoints

public int getNumDataPoints()

return expected number of data points.

Returns:

int

getGraphWidth

public int getGraphWidth()

return adjusted width of a curve panel

Returns:

int

convertX

public int convertX(long X,
                    int line,
                    int offset,
                    int width)

convert chromosome coordinate into screen coordinate,

Parameters:

X - double

line - int

offset - int

width - int

Returns:

int

See Also:

convertX(double,int,int,int)

convertX

public int convertX(double X,
                    int line,
                    int offset,
                    int width)

convert chromosome coordinate into screen coordinate, according to the line number, offset and panel width

Parameters:

X - double

line - int

offset - int

width - int

Returns:

int

updateCurrPosition

public void updateCurrPosition(java.lang.String s)

Parameters:

s - String

See Also:

CursorInfoPanel.setPosition(String)

updateContig

public void updateContig(java.lang.String s)

Parameters:

s - String

See Also:

CursorInfoPanel.setContig(String)

getDisplayPanel

public DisplayPanel getDisplayPanel()

getDisplayPanel

Returns:

DisplayPanel

getDetailsAction

public javax.swing.AbstractAction getDetailsAction()

return detailsAction2

Returns:

AbstractAction

See Also:

DetailsAction

setDetailsActionEnabled

public void setDetailsActionEnabled(boolean flag)

call setEnabled(boolean) for detailsAction and detailsAction2

Parameters:

flag - boolean

getSettingsAction

public javax.swing.AbstractAction getSettingsAction()

return settingsAction2

Returns:

AbstractAction

See Also:

SettingsAction

getRemoveAction

public javax.swing.AbstractAction getRemoveAction()

return removeAction2

Returns:

AbstractAction

See Also:

RemoveAction

getStatAction

public javax.swing.AbstractAction getStatAction()

return statAction2

Returns:

AbstractAction

See Also:

StatAction

getVersion

public java.lang.String getVersion()

getVersion

Returns:

String

enableGUI

public void enableGUI()

call setEnabled(true) for all components joined with action

disableGUI

public void disableGUI()

call setEnabled(false) for all components joined with action

setParam

public void setParam(java.lang.String param,
                     java.lang.Object val)

replace an object in the parameters Map

Parameters:

param - String

val - Object

getParam

public java.lang.String getParam(java.lang.String parName,
                                 java.lang.String defValue)

try to get String from Map parameters, then from applet getParameter(String) or return default value

Parameters:

parName - String

defValue - String

Returns:

String

getParam

public int getParam(java.lang.String parName,
                    int defValue)

try to get integer from Map parameters, then from applet getParameter(String) or return default value

Parameters:

parName - String

defValue - int

Returns:

int

setDebugLevel

public static void setDebugLevel(java.lang.String dLevel)

debugInit = "1" or "init" debugProgress = "2" or "progress" debugComm = "4" or "comm" debugAction = "8" or "action" debugException = "16" or "exception" debug All = 1|2|4|8|16 or "all"

Parameters:

dLevel - String

getChromSize

public long getChromSize(java.lang.String chr)
                  throws VGBException

Return chromosome size. First try to find chromosome info in the applet records, id failed, try to ask server about the chromosome.

Parameters:

chr - String

Returns:

long

Throws:

VGBException

getChromSize

public long getChromSize()
                  throws VGBException

return size of current chromosome or contig

Returns:

long

Throws:

VGBException

release

public void release()

Do some work and refresh panels after slow operations, like data pulling

setReady

public void setReady(boolean f)

Parameters:

f - boolean

See Also:

isReady()

isReady

public boolean isReady()

Returns:

boolean

See Also:

setReady(boolean)

run

public void run()

Main thread of the applet. Doing lots of things. At start time pulls al configuration files from our server, creates important panels, creates instance of CommUnit and starts data pulling. During lifetime manages three timers and applet size. Updates information from server when the applet is idle.

Specified by:

run in interface java.lang.Runnable

upDate

public void upDate()

currently Not used Check server for new and deleted curves and new versions since start time.

See Also:

up2date(String)

windowClosing

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

Stop dataPuller thread when closing

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - WindowEvent

windowClosed

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

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowOpened

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

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowIconified

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

Specified by:

windowIconified in interface java.awt.event.WindowListener

windowDeiconified

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

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowActivated

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

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowDeactivated

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

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

resetCounter1

public void resetCounter1()

start 20 min counter

resetCounter2

public void resetCounter2()

start 30 sec counter

resetCounter3

public void resetCounter3()

start 0.5 sec min counter

isIdle1

public boolean isIdle1()

return true if idle more than 20 min

Returns:

boolean

isIdle2

public boolean isIdle2()

return true if idle more than 30 sec

Returns:

boolean

isIdle3

public boolean isIdle3()

return true if idle more than 0.5 sec

Returns:

boolean

freezeCounters

public void freezeCounters(boolean f)

Stop applet timer

Parameters:

f - boolean

getRandomString

public static java.lang.String getRandomString(int length)

return string of specified length with rndom content

Parameters:

length - int

Returns:

String

getAddAction

public javax.swing.AbstractAction getAddAction()

return addAction3

Returns:

AbstractAction

checkCurves

public void checkCurves(java.lang.String pos)

Method checkCurves starts separate thread, check curves for visibility and set visibility rules for displayed curves

Parameters:

pos - String

See Also:

CommUnit.checkCurves(Vector, String)

refreshOrgList

public void refreshOrgList()

refresh organism list in the pull-dawn menu

getHistory

public History getHistory()

Return history object

Returns:

History

getSwapCurvesAction

public SwapCurvesAction getSwapCurvesAction()

swapCurves

public void swapCurves()
                throws java.lang.Exception

Switch base genome. Works if only one curve is selected.

Throws:

java.lang.Exception

setUCSCActionTip

public void setUCSCActionTip(java.lang.String tip)

Set ToolTip for UCSC action button and menu.

Parameters:

tip - String

testPosition

public void testPosition(int minx,
                         int maxx)

testPosition

Parameters:

minx - int

maxx - int

getDialogElement

public Element getDialogElement(java.lang.String name)

Retern Element from XML Document from dialogs.xml

Parameters:

name - String

Returns:

Element

setNewSize

public boolean setNewSize(int width,
                          int height)

This method is called from JavaScript and sets new applet size. This doesn't happen in all browsers

Parameters:

width - int

height - int

Returns:

boolean

setNewWidth

public void setNewWidth(int nw)

setNewWidth

Parameters:

nw - int

See Also:

setNewSize(int,int)

setNewHeight

public void setNewHeight(int nh)

setNewHeight

Parameters:

nh - int

See Also:

setNewSize(int,int)

getNewWidth

public int getNewWidth()

return newWidth

Returns:

int

See Also:

setNewWidth(int)

getNewHeight

public int getNewHeight()

return newHeight

Returns:

int

See Also:

setNewHeight(int)

setSettingsVisible

public void setSettingsVisible(boolean b)

Enable or disable settings actions

Parameters:

b - boolean

enablePrinting

public void enablePrinting(boolean key)

enable or disable printing actions The only reason of using this method is bug in java 1.5

Parameters:

key - boolean

See Also:

PrintAction.run(), PrinterSetupAction.run()

setDangerous

public void setDangerous(boolean d)

Some actions set dangerous field in true in order to disable other actions. When the action is completed it must return dangerous to false

Parameters:

d - boolean

See Also:

isDangerous()

isDangerous

public boolean isDangerous()

return true if action can destroy the applet. So, the action must be disabled or delayed

Returns:

boolean

See Also:

setDangerous(boolean), startProgress(java.lang.String), stopProgress()

getPostHeader

public java.lang.String getPostHeader()

getPostHeader

Returns:

String

See Also:

SaveAsAction.saveData(OutputStream,ByteArrayOutputStream)