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