ATV - A Tree Viewer
Version 1.3 (November 2000)
Copyright (C) 1999-2001 Washington University School of Medicine
and Howard Hughes Medical Institute
All rights reserved
----------------------------------------------------------------


Since ATV is part of the forester framework it must be used in
conjunction with forester. 

The ".tar.Z" file is for Unix and Linux users.
The ".zip" file is for Microsoft Windows users.

Please email me at: zmasek@genetics.wustl.edu
for reporting bugs, comments, suggestions, complaints, ...


1. Obtaining forester/ATV
-------------------------

  ftp://ftp.genetics.wustl.edu/pub/eddy/software/

  http://www.genetics.wustl.edu/eddy/atv/




2. Unpacking forester/ATV
-------------------------

  Unix, Linux:

    "uncompress forester-1.3.tar.Z"

    followed by:
    
    "tar -xvf forester-1.3.tar"



  Microsoft Windows:

    Use a program such as WinZip to unzip "forester-1.3.zip".


  In both cases, a new directory named "forester-1.3" will
  be created in your working directory. This directory contains
  all the unpacked files. 



3. Running ATV
--------------

3.1. Running the ATV application
--------------------------------

ATVapp_awt requires Java 1.1.x or greater.

ATVapp requires either Java 1.1.x plus Swing, or Java 1.2 or greater.

There are two ways to run the application -- either directly from
the jar file ("ATVapp.jar" or "ATVapp_awt.jar", dependent on the
version of Java), or by compiling the source code.


  - Directly from the jar file: 
    ---------------------------
      Remark. Requires the Java runtime environment. If you do not
      have it, or if this does not work for other reasons, you can
      always compile the source code, as described below.



      o  for Java 1.1.x or greater:
         --------------------------
 
         "jre -cp ATVapp_awt.jar ATVapp_awt"

         in the same directory as ATVapp_awt.jar 
         (MS Windows users need to open a MS DOS prompt window)



      o  for Java 1.1.x plus Swing, or Java 1.2:
         ---------------------------------------
      
         "jre -cp ATVapp.jar ATVapp"

         in the same directory as ATVapp.jar
         (MS Windows users need to open a MS DOS prompt window)



  - Compiling the source code:
    --------------------------


      o  for JDK 1.1.x or greater:
         -------------------------

         compile with:

         "javac ATVapp_awt.java"

         in the same directory as ATVapp_awt.jar
         (MS Windows users need to open a MS DOS prompt window)


         then, to run ATVapp_awt:

         "java ATVapp_awt [name of tree file in NH or NHX format]"

         e.g. "java ATVapp_awt testtree.nhx" -- to display to
              tree which is part of this distribution	


	
      o  for JDK 1.1.x plus Swing/JFC, or JDK 1.2:
         -----------------------------------------

         compile with:
 
         "javac ATVapp.java"
        
         in the same directory as ATVapp.jar
         (MS Windows users need to open a MS DOS prompt)
	

         then, to run ATVapp:

         "java ATVapp [name of tree file in NH or NHX format]"

         e.g. "java ATVapp testtree.nhx" -- to display to tree
              which is part of this distribution	



  - Making life easier:
    -------------------

      Set your their CLASSPATH so that you can (e.g.) "java ATVapp"
      anywhere. For Unix/Linux use (example):

      "setenv CLASSPATH /path/to/forester"

      For Windows NT go to: "My Computer" | "Control Panel" | "System"
      | "Environment" and add to CLASSPATH.

      For Unix/Linux use (example)
      "alias atv 'java ATVapp'"
      to save some typing

      Windows users can modify the supplied example .bat file
      ("ATVapp.bat") and use it to start ATV with a mouse click
      on its icon.

      Obviously, all those commands are only examples, you need
      to modify them according to your directory structure and according
      to which version of ATV you are using and according to whether
      you are using the Java runtime environment.




3.2. Running the ATV Applet
---------------------------

Requirement: Java 1.1.x or greater.

File "ATVapplet.jar" needs to be placed into the same directory
as your HTML and your tree files (at least, this is the easiest
way, if you are more experienced with applets and HTML, you
will know what to do anyway).

You can obviously also compile the source code files with:
 "javac ATVapplet.java" 
and then use:
 "jar cf ATVapplet.jar [all resulting .class files]"
to create file "ATVapplet.jar" from the resulting .class files.

To use a ATV Applet in your web page, you need to place the
following into your HTML file: 

<APPLET ARCHIVE = "ATVapplet.jar"
 CODE = "forester.atv.ATVapplet.class"
 WIDTH = 200 HEIGHT = 50>
 <PARAM NAME = url_of_tree_to_load
  VALUE = place the URL of your tree file here>
</APPLET>


If you have more than one tree, it is easier to use Java script.

For an example, see
http://www.genetics.wustl.edu/eddy/atv/atvapplets/ATV_applets.html


For more information about ATV Applets please refer to the
documentation which is part of this distribution:
PDF:     "atv_documentation.pdf"
MS Word: "atv_documentation.doc"




4. Obtaining Java
-----------------

To download JDK 1.3 Standard Edition for Microsoft Windows:
http://java.sun.com/j2se/1.3/download-windows.html

To download JDK 1.2 Standard Edition for Linux:
http://java.sun.com/products/jdk/1.2/download-linux.html

To download JDK 1.2 Standard Edition for Solaris:
http://www.sun.com/software/solaris/java/download.html




5. More Information
-------------------

ATV documentation:
  PDF:     "atv_documentation.pdf"
  MS Word: "atv_documentation.doc"


API specification for forester (HTML): 
  is in directory named "forester_API_specification":
  point your browser to "index.html"
  Or online at:
  http://www.genetics.wustl.edu/eddy/atv/forester_API_specification/
  

Java:
  http://java.sun.com/


Jar files:
  http://web2.java.sun.com/docs/books/tutorial/jar/basics/index.html


