 visualization	Add visualization plugin to color with horizontal bar per multiple annotation		3	medium					
 editor	check if objects are moved out of drawing boundaries and expand if so		4	low					
 editor	auto-calculate drawing board size on open		4	low					
-visualization	Add visualization plugin to display labels as LATEX, to display formulas	Martijn	4	medium					
+visualization	"Add visualization plugin to display labels as LATEX, to display formulas"	Martijn	4	medium					
 shell integration	double click on gmml file opens in GmmlVision	Martijn	5	medium					
 visualization	Enable anti-aliasing for icons		5.1	medium					extra dll file needed in windows!
 visualization	Increase icon size to 64x64/128x128		5.2	low					
 visualization	Find optimal font size for labels (to fit in gene box)		6	medium					
 gdb	support using multilple gdb's at the same time		7	medium					specify priority for which database to search first
 gdb	remove dependency on ENSEMBL Gene		8	medium					
-editor	undo/redo, more sophisticated solution: only store objects that are changed		9	medium					
+editor	"undo/redo, more sophisticated solution: only store objects that are changed"		9	medium					
 visualization	export function to html/bmp/pdf		10	medium					
 gdb	gene database editor (e.g. To edit 'others' table)		11	medium					first look for generic hsqldb editor
-UI	Multiple documents: open multiple pathways, by split-window button		12	medium					
+UI	"Multiple documents: open multiple pathways, by split-window button"		12	medium					
 help	internal help viewer		13	medium					look for standard solution in SWT
 statistics	Gmml from R: create API that can be called from R		14	medium					
 command line	batch mapping		15	low					

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	

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	
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	
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	
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					
