Source Code Reference Guide

This file still needs to be updated to the new server.

Current as of December 2002.

The biocore directory looks like:

-rw-r--r--   1 buser bgroup        186 Nov 21 14:46 README
-rw-r--r--   1 buser bgroup      27167 Nov 22 11:02 build.xml
drwxr-xr-x   7 buser bgroup        516 Dec  4 17:56 applets/
drwxr-xr-x   2 buser bgroup        459 Dec  4 17:56 distFiles/
drwxr-xr-x   5 buser bgroup        508 Dec  4 17:56 externalAPI/
drwxr-xr-x   6 buser bgroup       2712 Dec  4 17:56 src/
drwxr-xr-x  11 buser bgroup        883 Dec  4 17:56 web/          
  • README - Simple text readme file.
  • build.xml - The ant configuration file. Explains all of the various options that you can give ant; explains how to compile with what dependencies, etc.
  • applets/ - Source code for applets.
  • distFiles/ - Files that get copied into distributions that are generated when doing an ant dist. Very very few people will need to modify anything in this directory.
  • externalAPI/ - Code for the various flavors of the external APIs are in the directory.
  • src/ - Servlet source code.
  • web/ - Files that are served by tomcat that are not servlet related. This includes various html, image, and jar files. BioCoRE specific tomcat configuration files are also found in this path.


The applets/ directory looks like:

-rw-r--r--   1 buser bgroup        398 Dec  5  2001 signjar
drwxr-xr-x   3 buser bgroup        183 Dec  4 17:56 VMD/
drwxr-xr-x   2 buser bgroup        700 Dec  4 17:56 ApplicationRunner/
drwxr-xr-x   3 buser bgroup       1980 Dec  4 17:56 NAMD_CFG/
drwxr-xr-x   7 buser bgroup        878 Dec  4 17:56 ControlPanel/
drwxr-xr-x   3 buser bgroup        383 Dec  4 17:56 swing_test/ 
  • signjar - Sample file that we use here for signing applets using netscape signing tools. You are free to modify for your own purposes.
  • VMD/ - Source code for the VMD launcher applet. This applet looks in a few common spots for a VMD executable on the user's computer and launches VMD with a special command line that instructs it to communication with BioCoRE.
  • ApplicationRunner/ - Old source code for an applet that can launch applications for the user. Not currently in use.
  • NAMD_CFG/ - Source code for the NAMD Configuration File Generator. This applet can be used to create or edit config files for NAMD.
  • ControlPanel/ - Source code for the Control Panel applet. This applet is handy communication tool that is in constant contact with the BioCoRE server.
  • swing_test/ - Source code for the swing_test applet. The Control Panel is written using java Swing. Since browsers often don't have Swing, this applet is executed before the Control Panel applet. If the user has Swing, then the Control Panel is called. Otherwise, the user is given the opportunity to either install Swing (preferred) or use a temporary copy of swing, incurring a two megabyte download penalty.


Additional information the external API is available at:


The src directory contains:
  • The Java code files for a number of servlets. We have tried to keep the servlet code itself minimal with attending code in the TB/collab directory.
  • A util/ directory that contains utility classes used by all servlets.
  • The TB/collab directory which contains subdirectories pertinent to certain servlets.
  • The shared directory contains code that is shared between the servlets and applets. This lets java objects be easily transferred from server to client. The build.xml ant configuration file takes care of copying shared files around as needed.


The web directory contains:
  • applets/ - Jar files.
  • icons/ - Generic miniature icons used by the BioFS to denote file types.
  • updates/ - HTML files for update information for the BioCoRE code.
  • docs/ - BioCoRE documentation. (Not complete)
  • images/ - Various pictures used by the collaboratory.
  • VMD/ - A tcl script that is read by user's VMD sessions to connect back to BioCoRE.
  • html/ - Various html files that BioCoRE shows the user.
  • sounds/ - Various sounds that the Control Panel can use for notification.
  • WEB-INF/ - Tomcat specific directory. This directory isn't visible to users and contains web.xml which is used to define how the BioCoRE server interacts with Tomcat. In addition, certain external JAR packages are stored in the lib directory.


The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.