-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	
+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 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	
+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
+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	
+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	

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					
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	
UI	re-implement property table	Thomas						done	
UI	create view / edit mode	Thomas						done	
UI	create toolbar for drawing new graphics	Thomas						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					
