 property editor	adding geneproduct: option to search id in gdb	Thomas		low					
 gex	speed up caching gex data on loading mapp	Thomas		medium				done	using Derby (+/- 5 sec for average pathway)
 Packaging	stabilize API: use more getters / setters and private members	Thomas		medium					
-UI	Check for modification, ask to save when quitting program	Thomas		medium					
+UI	"Check for modification, ask to save when quitting program"	Thomas		medium					
 colorset	implement drag and drop	Thomas						done	
 colorset	add option to delete colorset / object	Thomas						done	
-colorset	get gradient data columns from gex	Thomas						done	
-colorset	add action colorsetmanager	Thomas						done	
-colorset	add combo in toolbar, select colorset	Thomas						done	
-colorset	speed up saving colorset on closing colorsetwindow	Thomas						done	
-colorset / drawing	color geneproducts by selected colorset	Thomas						done	
-criteria builder	create ui window	Thomas						done	
-criteria builder	implement 'color by gradient'	Thomas						done	
-database	open/close connection to db only at start and end of program	Thomas						done	
-drawing	fix retained selection	Thomas						done	
-drawing	disable sticky line ends on shape	Thomas						done	
-drawing	fix changing fontsize after subsequentially zooming	Thomas						done	
-drawing	re-implement selection box	Thomas						done	
-drawing	resize geneproduct labels when zooming	Thomas						done	
-drawing	zoom to fit	Thomas						done	
-drawing	fix selection box only works from topleft to bottomright	Thomas						done	
-drawing	make it possible to use mouse scrollbutton	Thomas						done	
-drawing	create mouse listener methods for drawing new graphics	Thomas						done	
-drawing	fix negative width/height of graphics elements	Thomas						done	
-drawing	fix flickering when moving objects	Thomas						done	
-drawing	implement double buffering for further flicker reduction	Thomas						done	
-drawing	fix deselect when pressing only handle of selected object	Thomas						done	
-drawing	clip text label in geneproduct (when too large)	Thomas						done	
-drawing	allocate coloring by expression in seperate gmmlgraphics class	Thomas						done	
-drawing	pre-load coloring data on opening mapp / gex	Thomas						done	
-drawing	add colorset legend (use colorsetpreview)	Thomas						done	
-drawing / gmml	ensure update of gmml document on changing graphics	Thomas						done	
-drawing / gmml	create new jdom element when creating new graphic	Thomas						done	
-drawing / gmml	add non-graphics attributes to updateJdomGraphics()	Thomas						done	
-drawing / gmml	fix color from and to gmml	Thomas						done	
-expression data	read gex to temporary database	Thomas						done	
-expression data	dialog option 'load gex'	Thomas						done	
-expression data	add expression data to gene info	Thomas						done	
-expression data	add 'convert gex' option	Thomas						done	
-expression data	change 'load gex' to 'select gex'	Thomas						done	
-gdb2hsqldb	write queries	Thomas						done	
-gdb2hsqldb	fixed file location / properties	Thomas						done	
-gdb2hsqldb	dialog option 'convert'	Thomas						done	
-gdb2hsqldb	thread / progress	Thomas						done	
-map gene info	write queries	Thomas						done	
-map gene info	create ui for displaying info	Thomas						done	
-map gene info	lookup gene when clicked	Thomas						done	
-property editor	add more geneproduct attributes to property editor	Thomas						done	
-property editor	sort labels in property editor	Thomas						done	
-property editor	custom labels in property editor (so not neccesarily attribute names)	Thomas						done	
-property editor	dropdownlist for choosing datasource on geneproduct	Thomas						done	
-select gdb	create select menu	Thomas						done	
-select gdb	test when db files moved	Thomas						done	
-UI	add save as	Thomas						done	
+colorset	get gradient data columns from gex	Thomas						done
+colorset	add action colorsetmanager	Thomas						done
+colorset	"add combo in toolbar, select colorset"	Thomas						done
+colorset	speed up saving colorset on closing colorsetwindow	Thomas						done
+colorset / drawing	color geneproducts by selected colorset	Thomas						done
+criteria builder	create ui window	Thomas						done
+criteria builder	implement 'color by gradient'	Thomas						done
+database	open/close connection to db only at start and end of program	Thomas						done
+drawing	fix retained selection	Thomas						done
+drawing	disable sticky line ends on shape	Thomas						done
+drawing	fix changing fontsize after subsequentially zooming	Thomas						done
+drawing	re-implement selection box	Thomas						done
+drawing	resize geneproduct labels when zooming	Thomas						done
+drawing	zoom to fit	Thomas						done
+drawing	fix selection box only works from topleft to bottomright	Thomas						done
+drawing	make it possible to use mouse scrollbutton	Thomas						done
+drawing	create mouse listener methods for drawing new graphics	Thomas						done
+drawing	fix negative width/height of graphics elements	Thomas						done
+drawing	fix flickering when moving objects	Thomas						done
+drawing	implement double buffering for further flicker reduction	Thomas						done
+drawing	fix deselect when pressing only handle of selected object	Thomas						done
+drawing	clip text label in geneproduct (when too large)	Thomas						done
+drawing	allocate coloring by expression in seperate gmmlgraphics class	Thomas						done
+drawing	pre-load coloring data on opening mapp / gex	Thomas						done
+drawing	add colorset legend (use colorsetpreview)	Thomas						done
+drawing / gmml	ensure update of gmml document on changing graphics	Thomas						done
+drawing / gmml	create new jdom element when creating new graphic	Thomas						done
+drawing / gmml	add non-graphics attributes to updateJdomGraphics()	Thomas						done
+drawing / gmml	fix color from and to gmml	Thomas						done
+expression data	read gex to temporary database	Thomas						done
+expression data	dialog option 'load gex'	Thomas						done
+expression data	add expression data to gene info	Thomas						done
+expression data	add 'convert gex' option	Thomas						done
+expression data	change 'load gex' to 'select gex'	Thomas						done
+gdb2hsqldb	write queries	Thomas						done
+gdb2hsqldb	fixed file location / properties	Thomas						done
+gdb2hsqldb	dialog option 'convert'	Thomas						done
+gdb2hsqldb	thread / progress	Thomas						done
+map gene info	write queries	Thomas						done
+map gene info	create ui for displaying info	Thomas						done
+map gene info	lookup gene when clicked	Thomas						done
+property editor	add more geneproduct attributes to property editor	Thomas						done
+property editor	sort labels in property editor	Thomas						done
+property editor	custom labels in property editor (so not neccesarily attribute names)	Thomas						done
+property editor	dropdownlist for choosing datasource on geneproduct	Thomas						done
+select gdb	create select menu	Thomas						done
+select gdb	test when db files moved	Thomas						done
+UI	add save as	Thomas						done
 UI	re-implement property table	Thomas						done	
 UI	create view / edit mode	Thomas						done	
 UI	create toolbar for drawing new graphics	Thomas						done	

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					
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					
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					
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	
