The Laj and Maj applets are written using Java 1.2 (a.k.a. J2SE 1.2), and theoretically any web browser that fully supports this should work. However in practice, browsers' built-in Java support tends to be outdated, inconsistent, and buggy, so for best compatibility we recommend that you download and install Sun's free Java Plug-in software in your browser. The main page for this product is http://java.sun.com/products/plugin/, and there is also a simplified download facility (latest version only) available at http://java.sun.com/getjava/, which provides automatic download and installation for Win+IE and a manual download page for other systems.
The plug-in is usually bundled with the Java 2 Runtime Environment (JRE) or the Java 2 Software Development Kit (SDK). If you are given a choice between these, either will do; the JRE is smaller because it doesn't include developer tools, but both of them contain the plug-in. Note that we have tested our applets with version 1.2.2 of the plug-in, but newer versions should also work. We have, however, observed some drawing anomalies with the 1.4.x series on some platforms, especially in Laj's symbolic panel for exons and repeats. Until this is debugged, you may want to stick with 1.2.x or 1.3.x.
Each download should come with installation instructions (read them!), but here are some additional platform-specific tips.
If you are running Windows 98-XP with Internet Explorer and want the latest version of Java, you can use the automated installation page at http://java.sun.com/getjava/; otherwise you can do a manual download from http://java.sun.com/j2se/downloads.html, which also has links to installation instructions. We recommend that you delete any previously installed versions of the plug-in, JRE, JDK, and/or SDK before you install the new one, to avoid getting them mixed. For example, in Windows 98 you can do this by opening the Start menu and choosing Settings - Control Panel - Add/Remove Programs, then selecting from the list the items you want to uninstall. After the new installation is complete, you may need to close and restart your browser to make it recognize the new plug-in, or even reboot your computer. Once installed, the plug-in works with both Internet Explorer and Netscape.
Currently Sun does not have a Java Plug-in for Macs, but Mac OS X ships with Java 1.3 already included, and Apple also has an implementation of Java 1.4.1 available for Mac OS X 10.2.3 or later via their Software Update mechanism or from http://www.apple.com/downloads/macosx/. Note that according to Apple's web site, 1.4.1 will be installed alongside 1.3.1 rather than replacing it, and although Safari will use 1.4.1 if it is installed, other browsers will continue to use 1.3.1. Both seem to work adequately with our applets. For Mac OS Classic, Apple has a Java runtime called MRJ 2.2.5, but unfortunately it only supports Java 1.1.8, not Java 1.2. For more information about Java on the Mac, see http://www.apple.com/java/ and http://developer.apple.com/java/.
Sun now provides versions of the Java Plug-in for Linux, in either RPM or self-extracting binary format, which you can download from http://java.sun.com/j2se/downloads.html. Be sure to read the installation notes first, for system requirements and detailed instructions.
Note that Solaris 8 already includes Java 1.2, though you may want to install a newer version. Sun provides versions of the Java Plug-in for Solaris, in self-extracting binary or tar.Z package format, for both Sparc and x86 processors. These are available at http://java.sun.com/j2se/downloads.html. Be sure to read the installation notes first, for system requirements and detailed instructions. In particular, note that you may need to apply some Solaris patches to your system before installing Java, and possibly obtain additional fonts. You might also want to uninstall any previous versions of the plug-in, JRE, JDK, and/or SDK to avoid getting them mixed. After the installation, you may need to close and restart your browser to make it recognize the new plug-in.
One last bit of advice: at one point during our installation, we were instructed to enter the command xhost + , but this is a bad idea because it seriously compromises your system security. If this message appears, we recommend using proper security protocols instead.
For availability of the Java Plug-in on other computers, see http://java.sun.com/cgi-bin/java-ports.cgi.