JMV 0.8 Development

JMV 0.8 Development Status

  • Working toward JMV 0.8 Pre-release
    • Updated README to include Licorice rep, and PUBSYNCH and HELPPAGE parameter info.
    • Updated README file, to include lib/ directory and version 0.80.
    • Updated the README file
    • Revised applet creator code to work with IE. It now creates the test applet correctly, to check if Java exists on IE.
    • The VRML library from Sun's Java3D fly-through demo program
    • Changed loadVRMLFile() to accept URLs.
    • Changed the classpath for vrml97.jar and jai_codec.jar to look in ../lib
    • Changed order of reps in the list.
    • I set up the Makefile so the testsign target now signs the applet with the test certificate I've created and stored in devkey.store. I gave the key a 365 day lifetime.
    • In initContents(), revised the layout, so the Applet uses BorderLayout and the controls use a GridBagLayout, instead of determining Bean position by exact coordinates.
    • Changed "Publish" and "Synch" buttons to "Save session" and "Load session", respectively.
    • Fixed a bug where if you loaded a vrml file, and then a pdb file, the pdb file would not be displayed until you changed representations.
    • Added Licorice option and changed default help URL.
    • Added convenience function getPosition(), which defaults to time 0. Added function findAtomInResidue() for future use in Ribbons, Cartoon reps.
    • Also added support for writing a jpeg when publishing a state.
    • Added new help pages.
    • Also added a main() function which which creates the applet in a MainFrame, allowing it to be run as an application.
    • Added support for a SoftHashMap, which stores Soft References to previous molecule representations. Added an m_strFilename parameter for a key to store the BranchGroup In drawMolecule(), first search the map for the key, (filename + representation), and return that if found. If not found, create it and add it to the hashmap.
    • Revised how the "Loading" and "Calculating" messages get displayed.
    • For JOptionPanes, set the parent parameter to be m_canvas instead of a new Container, since this was giving errors in Java1.4.
    • Re-added drawSpheres() and drawOneSphere() functions without the radScale parameter (it defaults to true).
    • Added soft-reference benchmarks to the benchmarks area.
    • Centered the textfield in the Load window Changed the titles of the Publish and Load windows When there is only one rep/color/gradient, sent this information to the MainBean through firePropertyChange().
    • In propertyChange(), revised synchronization so that it will save the rep/color/gradient when only there is only one in the syncronized state. Also, if a new file is loaded after a state with multiple reps has been loaded, JMV defaults to Tube, Index, RGB for the new molecule.
    • Added Licorice to the choice box.
    • Added Licoricerepresentation: Added LICORICE enumeration Added support for licorice in drawMolecule(), changeColorsInBranchGroup(), changeColors(), drawAtoms(). Revised drawOneSphere() and drawSpheres() to take an additional parameter, radScale: a boolean which is true if you want to scale the sphere based on atom type (VDW, CPK), and false if you just want to scale by the given "scale" parameter (Licorice).
    • Added HELPURL parameter to the applet so it opens http://www.ks.uiuc.edu/Development/jmv/JMVHelp.html for the help page.
    • Added JMVHelp.html to the CVS tree. It contains an FAQ on features and troubleshooting for JMV.
    • In init(), checked for a HELPURL parameter and set the url to the help page to be displayed in the HelpBean.
    • Added inputs for setting pub/synch and the help page url.
    • Added getUrl() and setUrl() methods for getting and setting the url to the help page
    • In JOptionPanes, changed the parent from a new Container to "this".
    • Benchmark code that creates spheres like the updated code in JMV. It creates a Shape3D with the Geometry of the Sphere rather than the Sphere object.
    • On IE, we do an initial check for the Java Plug-In using a dummy applet. This applet was causing errors, since it had no CODE parameter. I added a JMV as the CODE parameter, and added an ARCHIVE parameter so it could find it. I also added a TEST parameter, so it wouldn't actually do much. (JMV.java was changed to not do much if the TEST parameter existed.)
    • Added the ability to include or not include the PubSynchBean with a PUBSYNCH parameter in the applet.
    • In drawTrace(), revised the check for CA-atom list length.
    • In propertyChange(), added code to set representation back if the current state is MIX.
    • Removed "#import Molecule" statement since Java1.4 was complaining.
    • Removed synch(). Now we only use synchMulti(). Removed some System.out.println() statements.
    • Modified code for pub/synch; Replaced drawLineAtom() with drawLineAtoms(), which draws all the atoms in Lines representation as one BranchGroup, instead of each atom as a separate BranchGroup. Revised getColorArray() to get the proper colors for a paritally drawn Lines representation, such as one that has been loaded from a published file. Revised changeColors() to use changeColorsInBranchGroup(), so that separate BranchGroups in a published state are colored correctly. Removed drawCPKAtom() and revised the drawing of individual CPK atoms in a synch, so that the tree structure is the same as that of the original.
    • Updated web pages.
  • JMV 0.7 Pre-Release (10/30/2001)

Please email any questions to jmv@ks.uiuc.edu.