Copyright (C) 2003-2009 Institute for Systems Biology
                        Seattle, Washington, USA.

This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public
License along with this library; If not, see <http://www.gnu.org/licenses/>.
=======================================================================


This is a provisional readme file for BioVisualization, a set of  browser 
independent Google Visuailzation API compliant biology oriented visualizations 
implemented in javascript and actionscript 3. Please feel free to 
edit and expand it. If something you need to do is not covered here contact 
us and we will update it.

Before starting you should read the google Visualization API documents 
to learn the basics of creating a data table and using API compliant 
visualizations:
	http://code.google.com/apis/visualization/
	
Table of Contents

1.  Getting set up in Flex Builder and building code.
2. BioNetwork Parmaters
3. BioHeatmap Parmaters
4. Deploying on a server
5. Creating your own visualization using flexvistemplate
6. List of Dependencies

1.  Getting set up in Flex Builder and building code.

	-creat your own fork on github if you wish to develop against the code
	(see: http://github.com/guides/fork-a-project-and-submit-your-modifications)

	-check out from github using a command like: 
	git clone git@github.com:YOURUSERNAME/Lichen.git (if you have forked)
	git clone git://github.com/ryanbressler/Lichen (if you do not wish to fork)
	
	- open flex builder and go to file>New>ActionScript Project
	set the path to your Lichen dir and the name to Lichen
	and hit finish.
	
	- go to project>properties. Go to actionscript build path, and then go to the
	lib dir tab, click the add swc folder hit 'browse' button, and choose the 
	Lichen/lib sub dir.
	
	- Set bionetwork.as, bioheatmap.as or flexvistemplate.as as your default 
	executable (use theright click menu)
	
	- delete the contents of your html-template dir  and src/lichen.as 
	(to get rid of all auto generated stuff).
	
	- go to the Lichen dir in a shell and run: 
		git checkout html-template
	 to recreate the files in html-template from github.
	
	- Hit the build button and wait. A browser with bionetwork.html should come
	up, you can open any of the other html files at this point.
	
	- If you encounter a security zone error there are two possible fixes:
		1) Ensure there are no spaces in the path to the html file.
		
	 	2) Serve the Lichen/bin-debug directory with a web server then go to Project/Properties, 
	 	ActionScript Build Path, and set Output Folder URL to the URL where the bin-debug file 
	 	can be found (example: http://localhost/Lichen).
	
	- Make sure the swf is built in bin-debug. Then you 
	can go to bin-debug folder and open any html files under that folder.
	
	You may need to change the font family being embeded if your system does not have helvetica installed

2. BioNetwork Parameters
Documentaton had been moved to: 
http://ryanbressler.github.com/Lichen/bionetwork.html


3. BioHeatmap Parmaters
	http://ryanbressler.github.com/Lichen/bionetwork.html
		
4. Deploying on a server
	To deploy a visualization on a server you need to host the associated js and swf files. 
	Currentley, if you wish to host these files in a seperate directory you need to edit the path
	to the swf file in two places in the embed tag string. You can do this using find and replace 
	(EX bionetwork.swf -> /js/bionetwork.swf).
	
	We are looking for a more maintainable solution if anybody has any ideas.

5. Creating your own visualization using flexvistemplate

	The easiest way to start work on your own visualization is to create a copy of flexvistemplate.as,
	flexvistemplate.js and flexvistemplate.html. and use find and replace to update all occurences of
	flexvistemplate (should be mostly file names) and FlexVisTemplate (class names).
	
	After you have done this you can verify that everything is working using the debuger. Set your 
	new as file as the default executable, set a break point in the draw function after data import and 
	compile and run in debug mode.
	
6. List of Dependencies (Track Versions Here as we update)
	corelib.swc
		http://code.google.com/p/as3corelib/
	flare.swc
		http://flare.prefuse.org/
	com.clevr.*
		http://clevrlib.riaforge.org/
	FlexUnit.swc (Not currentley used?)