[Jtreeview-devel] JTV 1.0.9 released!

[Alok S. <al...@ca...>]

It's been a while, but there's a new version of java treeview. Main 
features:

- less memory consumption. ~50% of RAM for the same size files
- more stability. A lot of weirdness went away when I cleaned up the 
code to gear up for "The Future"
- optional registration.

As some of you know, we have submitted a grant, and it would be helpful 
to have some statistics on users. Click "No" if for any reason you 
don't want to register, and you should not be bothered until you 
download a new version. There's also a new Help->Registration... menu 
item where you can go and register if you change your mind. Or even 
register multiple times, but please don't do that, as it may confuse us 
and cause the reviewers to become suspicious.

For those who are curious, I will present here a rough, non-binding 
sketch of what might happen in the future. Please feel free to suggest 
any changes or additions, although I can't guarantee high priority.

Things to add in next few months:

	karyoscope: add postscript output						karyoscope: change "pixel per 
value" to y-zoom, add zoom in, out buttcons	karyoscope: change "pixel 
per map" to x-zoom, add zoom in, out buttcons	karyoscope: add overlay  
of multiple graphs in karyoscope	scatterplot: add postscript 
output						registration: add check to see that global xml config can 
be parsed/written, warn user if there is problem.	dendrogram: make sure 
that "compare with..." works
	dendrogram: document node-flipping and compare with... 
functionality	url linking: add note about escaping chars in windows 
URLs (Davin Townley-Tilson)	RAM: switch data model to floats instead of 
doubles to save RAM.	RAM: remove all refs to (String []) 
RectData.elementAt(i), use getString() instead.	general: change to MIT 
Open Source License				general: add check in makeTars that checks 
version in build.xml and TreeViewApp.	website: make web page with links 
to projects that use java treeview (GMOD, TAIR)	website: add k-means 
example to examples page			website: read over documentation to ensure 
that it is consistent with current application	

Bugs to fix in next few months:

	dendrogram: resolve node-flipping inconsistency
	dendrogram: fix selection triggered by opening "Find..." when no genes 
selected
	dendrogram: find doesn't always let you pop up summary.
	karyoscope: fix bug in export - yeast chr 16
	knnview: rename to kmeansview. Eclipse makes it easy!
	javadoc: during html generation, there are many (well, 73) warnings 
which should be looked at.

Things to do later:

	plugin architecture. make all views plugins, even dendrogram.
	add plugin for the SGT (http://www.epic.noaa.gov/java/sgt/index.html)
	use the SGT to allow arbitrary plots on karyoscope
	plugin for fuzzy clustering display
	implement GEO cluster browser helper application
	redo "knn" (actually k-means) so it uses normal tvmodel, dendroview, 
add group-by feature to dendroview
	try out new version of Your Kit Java Memory Profiler on JTV to find 
RAM leaks.