JalView 1.7.5b Installation document September 1998
-----------------------------------------------

Author: Michele Clamp (michele@ebi.ac.uk)
        EMBL-EBI
        Hinxton
        Cambs
        UK.


Requirements:
-------------
For the application version:
  JDK1.1 or higher

For windows users I recommend the IBM
java distribution available from

http://ww.ibm.com

For the applet version:
  Netscape4.05 (4.04 will do but there is odd scrollbar behaviour)
  IE4
  HotJava1.1
  
I heartily recommend using the latest version of Netscape you can get
your paws on as the JVM has speeded up (especially on the graphics 
side) in the most recent versions.  I really, really don't 
recommend Netscape3 as things don't behave as expected and the
speed is abysmal.

Tested Platforms:
-----------------

For the application version:
   IRIX + SGI JDK1.1.2
   Win95 + Sun JDK1.1.5
   
For the applet version:
   Netscape4.05 on IRIX
   Netscape4.05 on win95
   IE4 on win95

   Netscape3 is no good - problems with fonts and dialog boxes.
   Netscape4.05 on Mac PowerPC - works but odd fonts.
   

I should expect most platforms to run JalView if you have either java1.1, 
Netscape4.05 or IE4.  If you have problems email me with the details.


Unix Application Installation:
------------------------------

1. You should have downloaded a file jalview-1.7.5b.tar.gz .  Gunzip and untar 
this file as follows

gunzip -c jalview-1.7.5b.tar.gz |tar xvf -

This will create a directory jalview-1.7.5b.

2.  cd to this directory and you should find the following files:

       INSTALL          -   This file!
       README           -   General info about obtaining jalview
       LICENSE          -   The gnu public license
       doc/             -   help files.
       examples/        -   example alignment files and html files.
       jalview.jar      -   the java classes (closest thing to a java executable)
       Jalview          -   the script file to run jalview
       Jalview.bat      -   windows script file (not used)

3.  Edit the file Jalview to reflect your java environment:

To run jalview you need to set the java environment variables.
Assuming a JDK is already installed you need to change two lines
in the script file Jalview .

You need to know where your java JDK is (or JRE) and then set up your
CLASSPATH variable so it can see both jalview.jar and the JDK classes.

You then need to set the JAVA_EXE variable to where your java binary 
lies.

e.g.

setenv CLASSPATH /usr/local/java/jdk-1.1.2/classes:<path to jalview>/jalview.jar
setenv JAVA_EXE /usr/local/java/jdk-1.1.2/bin/java

or

setenv CLASSPATH /ebi/supported/jdk-1.1.5/lib/classes.zip:<path to jalview>/jalview.jar
setenv JAVA_EXE /ebi/supported/jdk-1.1.5/bin/java

4.  Test the application as follows

Jalview examples/lipase.msf MSF 

This should print some twaddle to the terminal and bring up a
jalview frame with the alignment in.

If the format type is omitted then jalview assumes MSF format.
Other formats are FASTA, PIR and CLUSTAL


Windows application installation:
---------------------------------

1.  Unzip the downloaded file jalview-1.7.5b.zip

This will create a directory jalview-1.7.5b .

2.  cd to this directory and you should find the following files:
       INSTALL          -   This file!
       README           -   General info about obtaining jalview
       LICENSE          -   The gnu public license
       doc              -   directory containing help files
       examples         -   directory with example alignment files and html files.
       jalview.jar      -   the java classes (closest thing to a java executable)
       Jalview.bat      -   a script file to run jalview
       JalviewJRE.bat   -   a script file to run jalview using the Java Runtime Environment
       Jalview          -   the unix script file (not used)

3.  Edit the file Jalview.bat to reflect your java environment:

To run jalview you need to set the java environment variables.
Assuming a JDK is already installed you need to change two lines
in the script file jalview .

You need to know where your java JDK is (or JRE) and then set up your
CLASSPATH variable so it can see both jalview.jar and the JDK classes.

You then need to set the JAVA_EXE variable to where your java binary 
lies.

e.g. Add these lines to your Jalview.bat file 

set CLASSPATH=c:\java\jdk-1.1.5\classes.zip;<path to jalview>\jalview.jar
set JAVA_EXE=c:\java\jdk-1.1.5\bin\javaes


3a. If you have the java runtime environment modify the file JalviewJRE.bat 
    and use that instead of Jalview.bat

4. Run a test application:

Start Menu->Run

type c:\path_to_jalview\Jalview.bat c:\path_to_jalview\examples\lipase.msf MSF

If things are working OK you should get a DOS box up with some output
in it then a java window should appear with the alignment in it.  There
should be a short (a few seconds) wait whilst Jalview calculates the
consensus sequence and colours the alignment accordingly.

5. Associating file types with jalview:
This assumes you don't already have a program associated 
with alignment files.  This example is for .msf files
only.  It should be obvious how to adapt for different
extensions

Open a 'My Computer' window.

Go to the menu option View->Options->File Types->New Type

Change the icon if you like by pressing the "Change Icon"
button. (I haven't included icons in the distribution)

Put the following entries in the boxes:

  Description of type:    GCG Alignment Format

  Associated extension:   .msf

Now press the "New" box underneath the big "Action" box

  New:   
	Action:   open
	Application used to perform action: 
           c:\path_to_jalview\jalview.bat "%1" MSF

Press OK until both dialogs are closed and Bob's your 
uncle.  Double clicking a msf file should run jalview
for you.



  

   























