 colorset	refresh coloring when opening new mapp	Thomas						done	
 colorset	refresh coloring when edited colorset	Thomas						done	
 colorset	colorsetWindow: fetch datacolumns from cache and filter out string columns with gradient	Thomas						done	
-colorset	colorsetWindow: create options for colorset (indicate multiple values per gene, no criteria met..)	Thomas						done	
+colorset	"colorsetWindow: create options for colorset (indicate multiple values per gene, no criteria met..)"	Thomas						done	
 drawing	give drawing order to objects	Thomas						done	
 drawing / colorset	disable color by expression when editing	Thomas						done	
 gdb	create gene databases from ensembl	Thomas							partly done: human + mouse
-gdb / expression data	choose representative file for database (.properties), fix filechoosers	Thomas						done	
+gdb / expression data	"choose representative file for database (.properties), fix filechoosers"	Thomas						done	
 gex builder	import exprssion data from text	Thomas						done	
 gex builder	create ui window for gex import	Thomas						done	
 gui	add imageregistry for managing icons	Thomas						done	
 colorset	add error messages to color by criteria	Thomas						done	
 drawing	add delete function for graphics objects	Thomas 		medium				done	
-editor	handles on corners of drawing objects, no handle in center	Thomas	1	low				done	
+editor	"handles on corners of drawing objects, no handle in center"	Thomas	1	low				done	
 visualization	formalize API for visualization classes: plugin structure		1	medium					"3 visualization types: tooltip, drawing, sidepanel; choose and setup via colorset dialog"
 editor	scroll when moving object out of display		2	low					
 visualization	Add visualization plugin to add expression value(s) next to genebox		2	medium					

command line	help		17	low					
bug/misfeature	automaticly add name for new gradient/criterion	Thomas						done	
bug/misfeature	dropdownlist for new line: add normal line without dropdown	Thomas							
Packaging	Java webstart release	Martijn		medium					

Feature	Task	Who	Order	Priority	Orig Est	Curr Est	Elapsed	Remain
gdb	add CAS ids in GDB + backpage info	Martijn	1	medium				done
editor	add sidebar to add arbitrary text and store in gmml as comment or Cdata	Martijn	2	medium				
GMML format	Update XML schema to include keys for all elements	Martijn	3.1	high				done
GMML format	Modify converter to convert to new schema	Martijn	3.2	high				done
GMML format	generate default graphId's	Martijn	3.2	high				
GMML format	Modify gmml reader-writer to use new format. Possibly in a new branch?	Martijn	3.3	high				done
gmml visualization	add graphical representation for all supported GMML objects	Martijn	4.1	medium				
gmml visualization	use rotation field (add rotation handle)	Thomas	4.2	medium				done
gmml visualization	standarize fill and line color	Martijn	4.3	medium				
editor	"copy/paste of gmml objects, within program and outside program (as gmml)"	Martijn	5.1	medium				
editor	copy/paste as vector graphics	Martijn	5.2	low				
cytoscape	GmmlVision as Cytoscape plugin	Martijn	6	low				
mapp conversion	automatic conversion of GenMAPP mapps to Gmml	Martijn	7	low				
GMML format	Gmml / BioPAX integration -> add reaction information to links	Martijn	8	medium				
gmml visualization	MVC aproach for GmmlGraphics	Martijn	9	low				done
Packaging	Test app in linux	Martijn		low					
Packaging	auto-generate executable JAR and installer	Martijn		low				done	
search	add searchdialog/results to right sidepanel	Thomas	1	high				done	
search	mark found genes (add highlighted property)	Thomas	1	high				done	
user preferences	"Create general class + file to store user preferences (directories, gdb)"	Thomas	2	high				done	
user preferences	Create UI for editing preferences	Thomas	2	high				done	
editor	GMML from scratch (valid)	Thomas	3	high				"done, however gmml not valid yet"	
legend	Legend to sidepanel	Thomas	4	medium				done	
editor	multi-select: add resize handles to selectionbox	Thomas	5	low				done	
editor	multi-select by pressing CTRL	Thomas	5	medium				done	
help	"help as wiki-page (public), to open from help menu"	Thomas	6	high					
test	"user test: edit mapp, visualize data from tab-delimited text file"	Thomas	7	medium					end of september
drawing	align to gird	Thomas	8	low					
drawing	align/resize buttons	Thomas	8	low					
drawing	"undo/redo, quick solution: store entire drawing"	Thomas	9	medium				done by Martijn	
statistics	Design R objects to constrain structure of expression/pathway data	Thomas	10	medium				done	
statistics	Create example R-script to do create a simple top-list of pathways	Thomas	10.1	medium				done	
statistics	Create R-objects from GmmlVision and call R-scirpts from java	Thomas	10.2	medium				done	
