MZViewer - A Viewer for MZData files
------------------------------------

MZViewer is a free viewer for MZData format Mass 
Spectra (http://psidev.sourceforge.net/ms/).
It is provided in the form of a stand alone application, 
but also provides a java framework
which allows you to embed the viewer in your own 
java applications.


Installation
------------

The MZViewer application comes as a single zip 
file.  Simply unzip this into a suitable
directory to install the application.

As MZViewer is a java application you will need to 
have a suitable Java Runtime Environment
installed.  The software should work with Java >= 1.4.  
It has been tested with the Sun JRE v1.4 and 1.5 on 
Windows and MacOSX, but should in theory work anywhere.

If you don't have a runtime environment installed on 
your machine you can get one from http://java.com.

To lauch the application:

On windows: Double click the run_mzviewer.bat file

On MacOSX: There is a separate Mac Application bundle for 
this software. Just install and run the same way as any 
other application.

On other platforms: From within the MZViewer directory 
launch the following command

java -classpath .;./xercesImpl.jar;./xml-apis.jar uk.ac.bbsrc.babraham.mzdata.MZViewer



Embedding MZViewer in your own application
------------------------------------------

MZViewer relies on the Apache Xerces XML parser 
(http://xml.apache.org) so you will need to include this in 
your classpath for MZViewer to work (or substitue another 
appropriate parser).

To include MZViewer first create an 
uk.ac.bbsrc.babraham.mzdata.parser.MZDataReader object
(which takes either a String filename, a File, or a URL 
to an MZData file in its constructor) and then use this 
to create a GenericMSDisplay object which is an extension 
of JPanel and should display the Data.  Have a look at the 
MZViewer class to see how this was achieved in the stand 
alone application.


Bugs
----

This application has only been tested against a small set of 
MZData files.  If you find any bugs then please report them 
to our bug database at http://www.bioinformatics.bbsrc.ac.uk/bugzilla/
or send them to simon.andrews@bbsrc.ac.uk.