Setup instructions (hints):

Hints: if Eclipse doesn't work the way you expect, here's the usual suspects of Eclipse: 
	clean, close&open project, restart using -clean flag... 
	
	When eclipse is complaining about maven dependency jars: Please make sure that the given dependency 
	jar file is "visible" inside the eclipse project ("Maven Dependencies").
		If jar file dependency is missing: make sure to run ../mp2Dbuilder/installCDKIntoMaven followed by
		AND/OR project right-click->Maven->Update Dependencies.
		If jar file is present, but pom.xml is marked red: try editing the pom file, then Undo and Save 
		before running "clean project".
	


Make sure Maven2 Eclipse plugin is installed:
	Eclipse update site: http://m2eclipse.sonatype.org/update/
		Choose the following optional stuff (just to make sure):
			Central Repository index
			Integration for WTP
			POM Editor
			POM XML Editor

Apply jchempaint patches
	If there are patch files in the same directory as this readme file, then they should be applied
	to the jchempaint project:
	
	e.g. git am 0001-Added-generation-of-java-source-jars.patch  
	

Add jchempaint jars to local Maven repo

	cd mp2Dbuilder/.. (jchempaint directory is assumed to be placed parallel with this project)
	git clone http://pele.farmbio.uu.se/git/cdk-jchempaint.git/
	cd cdk-jchempaint
	git fetch origin (if there has been some time since the clone, i.e. resynching so that current branches will be visible)
	git checkout origin/14-bioclipse2.3.x -b bc14 (where bc14 is the name of your choice)
	ant clean (as a precaution)
	ant dist-all
	../mp2Dbuilder/installCDKIntoMaven (TODO: make Maven install script fail early if any jar installation fails)
	In Eclipse, do a refresh and "project clean" on mp2Dbuilder.
	In Eclipse, right-click mp2Dbuilder project and do a "Maven -> Update Dependencies", 
	 followed by "Run As -> Maven Clean" and "Run As -> Maven Install" 

Junit memory problem
	You may encounter a non-responsive GUI (such as a molecule area that remains black after pushing "GO").
	Firstly, make sure that it isn't a memory related problem by closing the showing window(s), and have
	a look at the JUnit tab in Eclipse. Should there be a heap space memory problem, please go to
	"Run As -> Run Configurations" and then look for the JUnit configuration of the failing test. Then
	choose the Arguments tab, and then fill the VM arguments field with "-Xmx512M" (without the quotes)
	before trying the JUnit test once again.
	
Maven build
	In Eclipse, right-clicking on mp2dBuilder project, choose "Run As"-> Maven clean, followed by "Run As"->Maven package.
	In its current incarnation, when performing the "package" goal of Maven, a jar will be built specifically 
	for the ReactSmartsMoleculeViewer being the main class.
	The resulting jar can be found in the target directory and can be executed by issuing the following command:
	java -Dcdk.debugging=true -jar mp2Dbuilder-0.0.1-SNAPSHOT-jar-with-dependencies.jar /home/podeus/dev/azWorkspace/mp2Dbuilder/src/test/resources/data/mdl/First500DB2005AllFields.rdf
	
Generating bin file
	run from inside the target directory:
	java -cp ./mp2Dbuilder-0.0.1-SNAPSHOT-jar-with-dependencies.jar \
	metaprint2d.builder.DataBuilderApp -i test-classes/data/mdl/First50DB2005AllFields.rdf \
	-o out.bin -rfile test-classes/data/mdl/ReactionSMARTSFilter.two
	
Testing resulting bin file
	run from inside the target directory (if you have metaprint2d-exe in your possession):
	java -jar ../../metaprint2d-exe-0.1-SNAPSHOT-jar-with-dependencies.jar \
	-d out.bin -c LOOSE "O=C(NC(=O)C)NC(=O)C(CC)(CC)Br"