DEVise JavaScreen Help

General

The DEVise (Data Exploration and Visualization) JavaScreen is a Java applet that allows users to interactively explore complex data sets. The JavaScreen applet connects to a DEVise server, which renders most images the user sees. This allows large data sets to be visualized without transmitting the full data set to the client applet.

Note that a full explanation of DEVise is beyond the scope of this help document. This document will focus on the areas useful to the average user of the DEVise JavaScreen.

Views

The view is the fundamental component of DEVise. A view is an area of the screen within which symbols are displayed, with each symbol corresponding to a record in the underlying data. One key property of a view is the axis ranges (which are in effect even if axes are not displayed in the view). Data outside the current axis ranges is not displayed. (Note that three-dimensional views are somewhat different in this respect.)

One of the most important features of views is that, in most cases, you can change the axis ranges by dragging with the mouse or by other actions. (See the "toolbar" and "keyboard shortcuts" sections below for specific information on how this is done.) Some views have their axis ranges "locked", to prevent changes that would render the visualization less usable. In some visualizations, several views have their axis ranges "linked", so that zooming in or out in one view will also zoom correspondingly in other views.

DEVise Cursors

The DEVise Cursor is a rectangular "box" within a view. The box can be moved (and in many cases, resized) by dragging it with the mouse. When you do this, "behind the scenes" connections will change another part of the visualization. In some cases, a DEVise cursor is used to select a region that is magnified in another view (this is probably the most obvious case). However, there are other uses of DEVise cursors, such as selecting which of a number of data sets to display.

A cursor can also be moved by clicking with the mouse on the place to which the center of the cursor should be moved. (This works even if the cursor is not within the view because the view's axis ranges were changed.)

Most DEVise visualizations are designed to be explored mainly by moving and resizing the DEVise cursors.

Toolbar

The Toolbar (located at the left edge of the JavaScreen) allows you to select from a number of different modes. These modes change the behavior of the JavaScreen as described below. In general, in order to perform a given action you have to select the appropriate toolbar mode, and then click or drag in the view that is to be affected. When you enter a given toolbar mode, the mouse cursor changes to reflect the current mode.

Note that some views may not allow all toolbar actions. In such cases, the mouse cursor will change to a no-op cursor. Also, at this time, the toolbar only has an effect on two-dimensional views.

• Drill down (show data records): in this toolbar mode, if you click on a data symbol, the location of the click (in data units) and the data associated with the symbol will be displayed. If multiple data symbols overlap or are very close together, the drill-down dialog will show the data corresponding to all of the symbols. If you click in an area in which there is no symbol, only the location of the click will be displayed.
• Show help for selected view: in this toolbar mode, if you click anywhere in a view, the help message for that view (if any) will be shown.
• Select cursor/zoom in XY/3D rotate: this is the "normal" toolbar mode. In this mode, you can drag or resize a DEVise cursor (if the mouse cursor is on a DEVise cursor). If you are not on a cursor in a two-dimensional view, dragging with the mouse will zoom in on both the X and Y axes (unless modified by keyboard shortcuts, see below). In a three-dimensional view, dragging with the mouse will rotate the structure (unless modified by keyboard shortcuts, see below). Also, a single-click in a view with a cursor will move the cursor to the mouse location. If there are multiple cursors in the view, only one will be moved.
• Expand DEVise cursor to fill view: in this toolbar mode, if you click anywhere in a view containing a DEVise cursor, the DEVise cursor in the view will be expanded (or contracted) to the dimensions of view axes. If there are multiple cursors in the view, only one will be resized.
• Increase symbol size: for some symbol types, the size can be varied. In this toolbar mode, clicking in a view with such symbols will increase the symbol size.
• Decrease symbol size: for some symbol types, the size can be varied. In this toolbar mode, clicking in a view with such symbols will decrease the symbol size. Note that the symbols cannot be made smaller than the "default" size, so the symbols will only be reduced in size if they have already been increased from the default.
• Home (show all data): in this toolbar mode, clicking in a view will set the view's axis ranges to the "home" setting. In most cases, this means that the view will be expanded (or contracted) to exactly the ranges required to show all data in the view. In some cases, there is a pre-defined home setting different than this default. Note that if the view is already at the "home" setting, performing this operation again will have no effect.
• Toggle axis ranges: in this toolbar mode, clicking in a view will toggle back and forth between the last two sets of axis ranges.
• Zoom in XY: in this toolbar mode, dragging with the mouse zooms in on both the X and Y axes. Single-clicking zooms in on both axes by a factor of two.
• Zoom in X: in this toolbar mode, dragging with the mouse zooms in on the X axis only. Single-clicking zooms in on the X axis by a factor of two.
• Zoom out XY: in this toolbar mode, dragging with the mouse zooms out on both the X and Y axes. Single-clicking zooms out on both axes by a factor of two.
• Zoom out X: in this toolbar mode, dragging with the mouse zooms out on the X axis only. Single-clicking zooms out on the X axis by a factor of two.

Keyboard shortcuts

Keyboard shortcuts are used by pressing the key while the mouse cursor is in the appropriate view. You do not have to select the view before pressing the key.

Axis Range Shortcuts

• 1 or End: zoom in on Y axis
• 2 or down arrow: move the Y axis range down
• 3 or Page Down: zoom out on Y axis
• 4 or left arrow: move the X axis range left
• 5: set the axis ranges to the "home" location (the default is to show all data)
• 6 or right arrow: move the X axis range right
• 7 or Home: zoom in on X axis
• 8 or up arrow: move the Y axis range up
• 9 or Page Up: zoom out on X axis
• Backspace: toggle between the last two axis range settings
• c or C: fit cursor to current axis ranges (cursor fills view)

2D Mouse Actions

• Click: select view and move cursor (if view contains a cursor)
• Drag: move cursor (if on a cursor) or zoom in
• Control-drag: X-only zoom (if not on a cursor)
• F1: toggle display of help information for the current view

3D Mouse Actions, Jmol view

Note that a Jmol view is one that shows both atoms and bonds.

• Left drag: rotate object
• Left click on atom (in drill-down toolbar mode): drill down (show associated record values)
• Control-right drag: move object
• Right click: show Jmol popup menu
• Control-left click: show Jmol popup menu
• Double-left click on atom: go into distance measurement mode
• Shift-drag, left/right: rotate object in the plane of the screen
• Shift-drag, up/down: zoom in (move mouse down) or out (move mouse up)
• Alt-drag: same as shift-drag
• Scroll wheel: zoom in (scroll down) or out (scroll up)

3D Mouse Actions, non-Jmol view

• Left drag: rotate object
• Control-drag: zoom in (move mouse down) or out (move mouse up)
• Alt-drag: move object
• Shift-drag: move object (same as Alt-drag)

Other 3D Shortcuts, non-Jmol view

• r or R: reset coordinate system to default

Symbol Display Shortcuts

2D views only.

• +: increase symbol size
• -: decrease symbol size
• v or V: toggle display of data values as text superimposed on symbols
• s or S: toggle display of symbols (disabled)

Version history

Version 5.9.2

• Fixed a bug that caused it to be impossible to move a cursor that's entirely outside the axis ranges of its view.

Version 5.9.1

• Disabled alt and shift mouse action modifiers in 2D views to prevent confusion (often caused by the JavaScreen not receiving key-up events from browsers).
• Moved the JavaScreen version history to the help page.

JavaScreen 5.9.0

• The JavaScreen now has a toolbar that provides an alternate way of performing a number of functions that previously could only be performed by key actions.
• Added fairly extensive help information to the JavaScreen.
• The code for loading icon images, etc., has now been improved and works universally for running from both jar files and individual class and image files.
• Added a button to show the Jmol selection trees without having to go into a menu.
• The JavaScreen now prints various useful information, such as the Java version, OS version, etc., at the beginning of the Program Information log.
• Configuration for the Florence mirror has been updated.
• Fixed JavaScreen startup scripts to deal with new dynamic libraries in CentOS.

JavaScreen 5.8.2.1

• Fixed a bug (954) that caused the JavaScreen to lock up the browser when leaving the JS page, if the Java plugin was version 1.6.

JavaScreen 5.8.2

• Moved status lights and mouse location info to the bottom of the window for cleaner appearance.
• The background color of the entire view area (the "screen background" color) is slightly contrasting.
• Added the sbgcolor applet parameter to set the "screen background" color, since this is now more prominent.
• Added some extra GUI-thread-related diagnostic output.

JavaScreen 5.8.1

• Fixed (or at least reduced) the lockup problems seen in 5.8.0.

JavaScreen 5.8.0

• Completely changed the JavaScreen color scheme and some other aspects of its appearance, to a more clean, modern look.
• Changed applet parameter names for colors from "fgcolor" and "bgcolor" to "fgcolor2" and "bgcolor2" so existing web pages don't override the colors.
• Structure selection tree window now comes up closer to the upper left corner of the screen in Jmol visualizations.
• Added client-only install option.

JavaScreen 5.7.2

• Added the capability to disable drill-down in Jmol views (to avoid accidental drill-down).
• Updated configuration for NMRFAM.
• Set things up so that "special" arguments (e.g., font path) to Xvfb are configurable.

JavaScreen 5.7.1

(With DEVise 1.9.0)

• Added drill-down capability in Jmol views.
• Added the capability to have a description that's different from the associated URL in the JavaScreen drill-down dialog (the value must be of the form "{description}{url}".
• Added the capability to have attributes that don't show up in the JavaScreen drill-down dialog (the attribute name must end with "_nodd").
• Added "clickable URL in JavaScreen drill-down dialog" feature (attribute name must end with "_url").
• Added Jmol version to the JavaScreen Option dialog.

JavaScreen 5.7.0

(With DEVise 1.9.0.)

• Added the option to render 3D molecules with Jmol: - Jmol is embedded within the JavaScreen. - Added Jmol menus to the JavaScreen menu bar. - Added trees to select which atoms are shown and highlighted within Jmol.
• Improved fonts -- larger, buttons/menus are now sans-serif.
• A number of improvements to debug logging and restarts.
• Added timestamps to many more items in the JSPoP debug output.
• A bunch of changes to improve restart logging, etc.:
  • Better error messages in jss.java.
  • Set maximum memory for all production Java server processes to 256 MB (because of weird problems on marlin.bmrb.wisc.edu).
  • DEVise.jspop and DEVise.jspop.loc send all start_devised output to a log file instead of to /dev/null.
  • check_jspop now puts check_connect.err.* in logs and doesn't delete it when there's an error.
  • run_check puts starting timestamp at beginning of output, saves output from failed tests to logs.
  • start_devised generates more output, now that it's being saved.
  • Better error messages from check_jsall, check_jspop, and check_jss.

JavaScreen 5.6.1

• Fixed JavaScreen client problems related to bug 992 (drill-down on empty data source crashes DEVise).

JavaScreen 5.6.0

(With DEVise 1.8.0.)

(Entries below here also included in 5.7.0.)

• JS now sends 3D coordinate updates only when it really needs to (when it's a collaboration leader).
• Changed configuration for "regular" and "wavelet" JavaScreens to kill Xvfb (since most of the JSPoP restarts these days seem to be because Xvfb gets goofed up).
• Changed the subject of error emails from run_check to put the JS ID and machine name closer to the beginning, so they show up better.
• Changed JavaScreen scripts from sh to bash because of problems at Osaka -- their sh didn't accept the -e test.

JavaScreen 5.5.2

(With DEVise 1.7.19.)

• Check_jspop now always deletes the check_connect.err.* file.
• Improvements to JS usage statistics script: now deals with the fact that the logs seem to be in local time instead of GMT; error messages if parsing time fails; prints a warning if there's no JSPoP pid file.
• Changed JavaScreen config files to work on teal instead of pumori.
• Run_check now touches a file in /tmp/.X11-unix to make sure that directory stays "fresh" and doesn't get deleted.
• Added dev_vis.loc for JS to use local sessions, etc., that come with standard DEVise distribution; DEVise.jspop script makes the "base" session temp directory.
• Added config file for BMRB Italy mirror.
• Added DEVise.jspop.loc that runs with the "local" sessions, etc.
• Added scripts to report JS usage on teal.
• We now exclude any host name *starting* with localhost from the "real" session open statistics.
• Added new options to JavaScreen configuration so we don't have to rely on there being a /p/devise.
• New config file for framenet.cs.wisc.edu (new server).
• Added JS usage script for framenet.
• Got DEVise/JavaScreen to work on basslet by turning off hangCheck.
• More improvements to the JSPoP debug logging.
• A possible fix to some of the JSPoP hangs we've been experiencing.
• More fixes relating to the JSPoP hanging problems on pumori.
• More diagnostic output.
• More JSPoP reliability improvements.
• JSPoP reliability improvements (no longer experimental).

JavaScreen 5.5.1

(With DEVise 1.7.18?)

• Much-improved JSPoP debug logging capabilities.
• Removed DEViseJSLoader references from html files, jsa or jsb is now loaded directly (fixes "half-screen" problem seen on Windows).

JavaScreen 5.5.0

• Restart_jspop gives an explicit error message if there's no bin2 directory.
• "Option" dialog now displays JSPoP and DEVise version, and JSPoP ID.
• JSPoP prints version and arguments to log file at startup.
• New version of JavaScreen usage stats script gets info from jspop.usage.* files, gives non-UW counts.
• Fixed a collaboration bug (race condition could cause a wrong command to get sent to the devised).
• Support for alternate colors for printing.
• Changed most buttons in the JavaScreen GUI to menus (to save space in preparation for adding new functionality).
• We now report the system's uptime on a JSPoP restart, so we can tell when restarts are triggered by system reboots.
• Non-applet JS now continues without dialog if it can't get the animation symbols.
• Fixed bug 889 (erroneous JSPoP restarts seen at BMRB because hostname lookup took an extremely long time).
• (Temporary) Extra debug output to try to track down recent JSPoP restarts.

JavaScreen 5.4.2

• Non-applet JS now continues without dialog if it can't get the animation symbols.
• Fixed bug 889 (erroneous JSPoP restarts seen at BMRB because hostname lookup took an extremely long time).

JavaScreen 5.4.0

• Restart_jspop gives an explicit error message if there's no bin2 directory.
• "Option" dialog now displays JSPoP and DEVise version, and JSPoP ID.
• JSPoP prints version and arguments to log file at startup.
• New version of JavaScreen usage stats script gets info from jspop.usage.* files, gives non-UW counts.
• Fixed a collaboration bug (race condition could cause a wrong command to get sent to the devised).

JavaScreen 5.3.0

(With DEVise 1.7.15?)

• JSPoP (but not JSS or DEVised) now use a new CircularLog class, so the log file doesn't grow out of control.
• Session opens are now logged in a separate JS usage log.
• All sessions with any hidden directories in their paths are now hidden in the session lists returned to the JavaScreen (for (for BMRB visualization server -- allows a session in a hidden directory to be opened by passing in the name, but then the user can't see any other sessions in that directory).
• There is now a configuration option to kill Xvfb when killing the JSS (to deal with the problem that once in a while Xvfb gets itself goofed up and you cannot successfully restart the DEViseds unless you kill Xvfb first).
• Fixed bug 872 (double append to path in JS open session dialog).
• Minor improvements to the debug logs.
• Added closeSession() and openSession() methods to the JS applet for Wavelet-IDR.
• Added id, directory, and hostname header to JS usage stats.
• JSPoP debug log improvements to try to track down the cause of some DEVised restarts.
• JSPoP (but not JSS or DEVised) now use a new CircularLog class, so the log file doesn't grow out of control.
• Session opens are now logged in a separate JS usage log.
• Changed JavaScreen scripts so things work even if the user has CLASSPATH defined; restart_jspop gives warning if sleeping because of lock file.
• jss_savepid *always* tries to start Xvfb, in case the file in /tmp/.X11-unix is there in error; got rid of path stuff in run_check.
• Added closeSession() and openSession() wrapper methods to DEViseJSLoader (should have done that before).

JavaScreen 5.2.2

• Fixed bugs relating to axis drawing with axis multiplication factors other than 1.
• Made refreshAllData() and restartSession() methods in DEViseJSLoader, so that the Wavelet-IDR JavaScript code can call them.
• Fixed problems with JSPoP restarts overlapping.
• Script fixes so BMRB mirror sites can generate JS usage stats.
• Various updates to the BMRB mirror site installation instructions, including info on setting up the JS usage statistics.
• Fixed bug 866 (JSPoP hangs on bad collaboration name from follower).
• Fixed bug 870 (JS follower crash goofs up leader also).
• Made JS invisibility destruction timeout configurable; fixed some other problems with loading and re-loading the applet.
• JavaScreen startup scripts now set DEVised fontkludge argument automatically.
• Eliminated or reduced "Abrupt end of input stream reached" errors in the JSPoP on normal client exit.