Readme for GBOOST_GUI

GBOOST_GUI is a program visualizating the results of BOOST or GBOOST. Pathway graph and Manhattan plot 
are the two main visualization types for interaction records and marginal assoication result files from BOOST 
or GBOOST respectively. If you encounter any problems about using GBOOST_GUI, you are welcome to contact the author 
at timyung@ust.hk.

Software Requirements for GBOOST: (For visualization only)
Operating system : Windows 
Java Runtime Environment (Version) : 1.6 or above

Software Requirements for GBOOST: (For visualization and launching GBOOST x64 executable)
Operating system : Windows x64
Java Runtime Environment (Version) : 1.6 or above
CUDA Driver : 2.3

You should find the following files and folders under root directory of GBOOST_GUI:
	x64\					-- Folder for GBOOST win x64 executable
	lib\					-- Folder for libraries used
	dbfile\					-- Folder for database files used (including KEGG_2_snp_b129 and INTERSNP_1.0.7)
	sample_inputs\				-- Folder containing one set of input samples (For import option of GBOOST_GUI only)
	ReadMe					-- ReadMe documentation
	startGBOOST_GUI.bat		-- Executable bat script for Windows
	GBOOST_GUI.jar			-- Java Executable file

=====================================================================================================================
Quick startup Guide :

Inputs:
	Filename list file of the analysis								
		-- filenameList.txt (i.e. the file has one line only, simdata.txt)
	Corresponding SNP name files									
		-- simdatasnpname.txt
	Resulting interaction records (with prefix "output_")			
		-- output_InteractionRecord.txt
	Resulting marginal association file 							
		-- output_MarginalAssociation.txt
	
Pathway graph is generated from the resulting interaction records and Manhattan plot 
is generated from the resulting marginal association file. The "File" menu provides 
options for users to launch a new GBOOST process, import BOOST/GBOOST result files and 
output the visualization types of GBOOST_GUI as bitmap images.

In the pathway graph, each vertex is labelled by its pathway, snpname and marginal association score 
from GBOOST result files. Each edge is labelled by the Chi-square score from GBOOST result files. The
snpname is used as the key to retrieve the corresponding SNP record in the database (INTERSNP_1.0.7).

There are three tool windows providing a variety of features for the pathway graph.
-- The "DataToolWindow" provides funtions to filter records from the resulting interaction records.
-- The "NodeProperty" provides information of the selected vertex from the database (if any) 
-- The "PathwayGraphOption" provides miscellaneous options for
	tranformating the pathway graph,
	changing the vertices' and edges' appearance,
	labeling the pathway graph
	-- Selecting "Annotating" mode enables users add labels to the pathway graph.
		1. Dragging the mouse with the button adds rectanglar grids to the pathway graph.
		2. A input dialog for labels is prompted when users have right click on any place within the pathway graph.
		3. "Shift" + left click of mouse deletes a labe or a rectanglar grid with the nearest center.
		
In the Manhattan plot, it shows marginal association scores of all SNPs from resulting marginal assoication
file from BOOST or GBOOST.