Installation Instructions for ViewPoint and ViewDist
----------------------------------------------------

Both these utilities require the Java Runtime Environment (JRE) v 1.3 or later. 
This can be obtained from http://java.sun.com. You only need the JRE rather than 
the full Java Development Kit (JDK) to run these applications.

To ensure you have a version of the java runtime on your machine, and that it is 
correctly listed in your Path setting, open a terminal session (or command prompt 
in Windows (Start->Run, enter 'cmd') and type

java -version

You should get something like the following if all is working correctly:

java version "1.3.1_01"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.3.1_01)
Java HotSpot(TM) Client VM (build 1.3.1_01, mixed mode)

The ViewPoint and ViewDist utilities are supplied in a .zip file, which contains 
this Readme.txt file, and the two executables. The executables are .jar files and 
can be extracted from the .zip file to any suitable location on you file system. 
They should run by clicking on them from Windows Explorer, or by entering the 
following command at a command prompt:

java -jar ViewPoint.jar

java -jar ViewDist.jar

Both utilities contain a help option which gives detailed guidance for their use,
however when running them from the command line you can specify various options
which will take aeffect at startup. By adding the -help option to the commands
above, the command arguments will be shown. These are as follows:

For ViewPoint:
--------------

[-infile <input data filename>]
[-suggestive <suggestive score threshold (float)>]
[-significant <significant score threshold (float)>]
[-fixXaxis (X axis units set to max chromo length)]
[-plot <plot type U or M>]
[-help (usage)]

For ViewDist:
-------------

[-infile <input data filename>]
[-diffile1 <first difference filename>]
[-diffile2 <second difference filename>]
[-infoCol <info column number>]
[-scorecol <score column number>]
[-intObsCol <observation count column number>]
[-intModelCol <model column number>]
[-plottype <plot type: internal, normal, chi>]
[-help (usage)]


Good luck with using these utilities, and please let me have any feedback and 
suggestions for improvement or further developments.


Harry N.Beeby, QIMR 12/9/2005