Table of Contents
The following package are necessary:
Java 2 JDK 1.4 or Java 5 JDK 1.5 (http://java.sun.com/).
Apache Ant (http://jakarta.apache.org/ant) - not necessary if you are using Eclipse with a Windows PC (see below).
On Linux/Unix/OSX try to install Apache Ant using a package installer.
Subversion - The definitive svn documentation is at http://svnbook.red-bean.com/.
If you are using Eclipse, see Chapter 9, Using Eclipse.
In February 2006 Jmol converted to the subversion version control system for our source code repository, frequently referred to as svn. The svn repository is still hosted by SourceForge.
The current development version of the Jmol source code can be checked out using:
~/workspace$
svn checkout https://jmol.svn.sourceforge.net/svnroot/jmol/trunk/Jmol
This creates a directory called Jmol
where we work on the source code:
~/workspace$ cd Jmol
To know the status of your workspace relative to the current repository you can say:
~/workspace/Jmol$ svn status
To update your workspace to the current repository revision use the update command
~/workspace/Jmol$ svn update
After modifying local files for testing, you can throw away your local changes and revert your changes back to your checkout revision:
~/workspace/Jmol$ svn revert
After developing, compiling, and testing changes locally, you can commit your changes by saying:
~/workspace/Jmol$ svn commit
Sourceforge.net provides basic instructions how to use svn at this page http://sourceforge.net/docman/display_doc.php?docid=31070&group_id=1
The definitive documentation for subversion is at http://svnbook.red-bean.com/
The home page for subversion is at http://subversion.tigris.org/.
If you are using Eclipse, see Chapter 9, Using Eclipse. Otherwise read this section carefully. In additon to the prerequisites mentioned in Chapter 1, Prerequisites you will of course need the Jmol source code. It can be checked out from the subversion repository as described above.
Once you have all the prerequisites, Jmol can be built from the top source directory with the ant command.
On Linux/Unix/OSX type:
~/workspace/Jmol$ ant
Windows users not using Eclipse type:
C:\workspace\Jmol> ant
The development version of the Jmol application is normally run by simply executing the jmol script in the Jmol development directory.
The development version of the Jmol applet is normally run by copying the
built *.jar files into a test
directory and then running a web page that accesses them.
On Linux/Unix/OSX:
~/workspace/Jmol$ ./jmol
On Windows (not using Eclipse):
C:\workspace\Jmol> jmol
If you are using the Eclipse IDE, you can run the application and/or the applet from within Eclipse. This allows for simpler debugging. See Chapter 9, Using Eclipse for more information.
Your text editor should indent for you. If it doesn't then either learn how to enable it or get another editor.
Indentation level should be two spaces.
class Foo {
int someClassVariable;
Foo(int evenOrOdd) {
someClassVariable = 99;
}
...
}
Space characters should be used instead of tabs.
Assignment and arithmetic operators generally contain spaces on both sides.
a = b + c;
You are allowed to eliminate the spaces within expressions in order to make operator precedence more clear.
int cSquared = a*a + b*b;
Spaces follow commas in argument lists.
foo(a, 3.14159, "jmol");
Lines should be no more than 80 characters wide.
Open brace goes on the line that starts the block. Close brace goes on a line by itself.
if (condition) {
...
} else {
...
}
while (condition) {
...
}
Loop indexes start at 0, not 1.
The only valid comparison operators for loop
termination are < and >=
... anything else is probably a bug. If you are really
sure that it is not a bug then put a comment in
the code.
Use long descriptive variable names and method names. Do not be afraid of typing.
Line-by-line comments within the code are discouraged ... except in very special circumstances. If you put in lots of comments like this then you may find them deleted.
If you feel obligated to insert comments put them as javadoc before the function body.
If your code is changing then do not put in comments. Bad/outdated comments are worse than no comments.
You may want to look at The Elements of Java Style by Vermeulen, et al.
A Jmol release consists of both the application and the applet.
Presumably both will have been well tested. For release, we are generating
a number of JAR files using Java 1.1. This is to
provide compatibility with the Microsoft Java Runtime Environment.
In the Jmol-data CVS module directory
a number of test files are located for the input filters. All files below
that module should be checked prior to a release.
Distribution packages will be made for any platform for which a developer promises to provide support. File used to create packages should be commited to CVS under the Jmol/packaging directory. Currently the following packages are available:
Debian (by Daniel Leidert and Egon Willighagen)
RPM (by Miguel Howard)
This section is deprecated since Jmol has moved to svn.
See the Jmol Wiki.