The maxdSetup utility can automatically download and configure the latest version of maxdView.

If you do not want to use maxdSetup (or you want to customise the installation in a way not supported by the installer) then it is possible to download and execute maxdView manually using the following instructions:

• Manually installing maxdView for the first time
• Manually upgrading to a new version of maxdView

Installing maxdView for the first time

1. Make sure you have Java installed...

maxdView requires Java version 1.2.2 or better.

If you know that you already have installed a suitable version of Java then proceed to Step 2, otherwise take a detour here.

2. Get the JAR file...

Create a new directory (folder) called maxdView in your home directory

Download the current version of maxdView into this directory.

3. Unpack the JAR file...

The JAR file is a compressed archive format. Before maxdView can be run, this archive must be unpacked.

Java provides a program to do this. The program is called jar (which stands for Java ARchive).

Choose either: Microsoft Windows® environment or Unix-like environment.

You will need an MS-DOS window to access the command line. (sorry...)

• You need to know where the Java binary folder is.

  The location of Java depends on which Java environment you have installed. Normally it is in  C:\Java  or  C:\Program Files\Java . Within this folder will be a folder called bin .

  Sometimes the Java folder will contain a folder called  jdk1.x  or  jre1.x . If either exists, the  bin  folder is likely to be found within it.

  You can use the Windows® "Find" function to search for a file called jar.exe. This file should be located in the Java binary folder.

• Set the path to the Java binary folder

  C:\Windows> path c:\Java\jdk1.2.2\bin

  ( substitute your Java binary folder for the red text )

• Go to the directory in which you have downloaded maxdView

  C:\Windows> cd c:\"Program Files"\maxdView

  ( substitute your download folder for the red text )

• Run jar to unpack the file

  C:\Program Files\maxdView> jar xf maxdView.jar

  ( substitute the name of the JAR you downloaded for the red text)

  When you run this command, there should be a pause, but no screen output

• Verify that things have happened as planned

  C:\Program Files\maxdView> dir *.class

  ( lots of files should be displayed,if not,
  check that the jar program was found and
  that you typed the jar command exactly as shown )

• If it looks ok, proceed to Step 4.

3B. Unix-like environment

• You need to know where the Java binary directory is.

  This directory can be found within the directories that are created when Java is installed. It is always called  bin . It contains the Java executable programs such as the compiler and the virtual machine.

  If you have installed your own local copy of Java you will (hopefully) know where it is, e.g ~/Java/jdk1.3/bin.

  System wide installations are usually in  /usr/local/java ,  /usr/java ,  /home/java  or  /opt/java .

  Sometimes the java directory will contain a directory called  jdk1.x  or  jre1.x . If either exists, the  bin  directory is likely to be found within it.

• Go to the directory in which you have downloaded maxdView

  ~ % cd ~/biotools/maxdView/

  ( substitute your maxdView download directory for the red text )

• Run jar to unpack the file

  ~/biotools/maxdView % /usr/local/jdk1.3/bin/jar xf maxdView.jar

  ( substitute the Java binary directory for the purple text and
  the name of the JAR you downloaded for the red text )

  When you run this command, there should be a pause, but no screen output

• Verify that things have happened as planned

  ~/biotools/maxdView % ls *.class

  ( lots of files should be displayed,if not,
  check that the jar program was found and
  that you typed the jar command exactly as shown )

It is a good idea to create a script or batch file that starts maxdView. You can then create a menu entry or shortcut icon in your windowing enviroment that runs this script. This makes it easy to start maxdView without typing things in.

Choose either: Microsoft Windows® environment or Unix-like environment.

• Go to the directory in which you have unpacked maxdView

  C:\> cd c:\"Program Files"\maxdView

  ( substitute your maxdView installation directory for the red text )

• Start the java virtual machine

  C:\Program Files\maxdView> c:\Java\jdk1.2.2\bin\java -classpath . maxdView

  ( substitute the Java binary folder for the red text,
  make sure you include the full-stop between the words classpath and maxdView )

• Go to the directory in which you have unpacked maxdView

  ~ % cd ~/biotools/maxdView/

  ( substitute your maxdView installation directory for the red text )

• Start the java virtual machine

  ~/biotools/maxdView % /usr/local/jdk1.3/bin/java -classpath . maxdView

  ( substitute the Java binary directory for the red text,
  make sure you include the full-stop between the words classpath and maxdView )

Upgrading to a new version of maxdView

• Get the latest maxdView JAR file
  (from http://www.bioinf.man.ac.uk/microarray/maxd/download.html)

• Follow the instructions above as if you were installing for the first time. Overwriting your existing version with a new version will not affect your saved application preferences and other configurations (such as the Code Runner and Annotation Loader).