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miles [Fri, 15 Mar 2013 23:33:26 +0000 (23:33 +0000)]
working revision, including the view ontology capability. Colors changed
in the ontology viewer from blue -> yellow to blue -> green
svn path=/; revision=437
miles [Fri, 15 Mar 2013 22:42:37 +0000 (22:42 +0000)]
not sure if heatmap is working, wanted something to revert to
svn path=/; revision=436
elserj [Wed, 13 Mar 2013 21:16:12 +0000 (21:16 +0000)]
Added counts for obsolete terms and total number of terms
svn path=/; revision=435
elserj [Wed, 13 Mar 2013 21:10:53 +0000 (21:10 +0000)]
Added script that can take an obo file and tell you how many non-obsolete terms exist
svn path=/; revision=434
miles [Wed, 13 Mar 2013 01:11:04 +0000 (01:11 +0000)]
svn path=/; revision=433
miles [Wed, 13 Mar 2013 01:09:44 +0000 (01:09 +0000)]
Term printing is now woring in viewOntology.php, nothing else has
currently been implimented here. Still to do: Gene printing, cell
coloring
svn path=/; revision=432
miles [Tue, 12 Mar 2013 23:42:10 +0000 (23:42 +0000)]
Everything appears to be working, will now begin serious work on the
view ontology tool
svn path=/; revision=431
athreyab [Thu, 21 Feb 2013 05:12:18 +0000 (05:12 +0000)]
code for contact upload script
svn path=/; revision=430
athreyab [Wed, 20 Feb 2013 17:33:24 +0000 (17:33 +0000)]
image annotation db schema files - load sql script, workbench schema file and image
svn path=/; revision=429
athreyab [Wed, 20 Feb 2013 17:27:34 +0000 (17:27 +0000)]
html 5 based prototype for web view of image annotation data - folder contains several implemenations - decide on one later
svn path=/; revision=428
lingutln [Wed, 30 Jan 2013 00:09:54 +0000 (00:09 +0000)]
Commented out active learning code. By Nikhil.
svn path=/; revision=427
lingutln [Wed, 30 Jan 2013 00:08:07 +0000 (00:08 +0000)]
Commented incomplete ActiveLearning code. By Nikhil.
svn path=/; revision=426
lingutln [Wed, 30 Jan 2013 00:00:33 +0000 (00:00 +0000)]
Resolved list drop down problem in Windows machines. Done by Nikhil.
svn path=/; revision=425
preecej [Wed, 23 Jan 2013 23:55:41 +0000 (23:55 +0000)]
Included dimers, and left a commented line for equivalent SSR counts
svn path=/; revision=424
preecej [Wed, 23 Jan 2013 22:58:26 +0000 (22:58 +0000)]
First draft
svn path=/; revision=423
preecej [Wed, 23 Jan 2013 22:30:11 +0000 (22:30 +0000)]
Initial copy from B.sylvaticum version, unmodified.
svn path=/; revision=422
elserj [Thu, 27 Dec 2012 19:18:07 +0000 (19:18 +0000)]
Added new sources
svn path=/; revision=421
naithans [Fri, 21 Dec 2012 22:51:11 +0000 (22:51 +0000)]
simple entities changed from RiceCyc to reactome
svn path=/; revision=420
naithans [Fri, 21 Dec 2012 22:50:00 +0000 (22:50 +0000)]
simple entities are from reactome databse not from ricecyc
svn path=/; revision=419
naithans [Fri, 21 Dec 2012 22:49:22 +0000 (22:49 +0000)]
In the curated folder, three pathways related to GA Biosynthesis. Here the simple entities were changed from riceCyc source to the reactome existing entries.
svn path=/; revision=418
miles [Thu, 6 Dec 2012 00:56:49 +0000 (00:56 +0000)]
jump to cluster unbroken
svn path=/; revision=417
miles [Tue, 20 Nov 2012 23:53:06 +0000 (23:53 +0000)]
now all species requested will appear, regardless of relevance, in their
original alphanumberical order. much bug fixing. download as jpg working
again.
svn path=/; revision=416
miles [Mon, 19 Nov 2012 23:33:11 +0000 (23:33 +0000)]
Fixed species inclusion to show even irrelevant species if asked.
Improved summary of data.
svn path=/; revision=415
miles [Mon, 19 Nov 2012 19:29:42 +0000 (19:29 +0000)]
species inclusion check boxes now in a table. Revised instructions
slightly. Renamed important functions. Select and Deselect All buttons
implimented.
svn path=/; revision=414
preecej [Fri, 16 Nov 2012 00:05:58 +0000 (00:05 +0000)]
changed support email address from ...@palea to ...@plantontology.org
svn path=/; revision=413
preecej [Thu, 15 Nov 2012 22:16:49 +0000 (22:16 +0000)]
updated icons for AISO rename
svn path=/; revision=412
naithans [Fri, 9 Nov 2012 19:02:58 +0000 (19:02 +0000)]
Initial commit of Sushmas rtpjs
svn path=/; revision=411
elserj [Fri, 9 Nov 2012 18:55:41 +0000 (18:55 +0000)]
Added folder for Sushma
svn path=/; revision=410
preecej [Thu, 8 Nov 2012 23:36:21 +0000 (23:36 +0000)]
svn path=/; revision=409
preecej [Thu, 8 Nov 2012 23:35:34 +0000 (23:35 +0000)]
changed from SIA to AISO
svn path=/; revision=408
preecej [Thu, 8 Nov 2012 23:26:31 +0000 (23:26 +0000)]
svn path=/; revision=407
miles [Tue, 6 Nov 2012 00:52:45 +0000 (00:52 +0000)]
Species inclusion now working for webpage only. Clear box added.
svn path=/; revision=406
miles [Thu, 1 Nov 2012 18:30:39 +0000 (18:30 +0000)]
updated Heatmap.jar to reflect the same color scheme as the website.
species elimination working.
svn path=/; revision=405
miles [Fri, 19 Oct 2012 23:24:32 +0000 (23:24 +0000)]
Species elimination finally working, only from Main Page though. now
should be usable for further publications.
svn path=/; revision=404
miles [Wed, 17 Oct 2012 23:33:20 +0000 (23:33 +0000)]
added correctly sized and moving scrollbar
svn path=/; revision=403
miles [Thu, 11 Oct 2012 23:03:28 +0000 (23:03 +0000)]
svn path=/; revision=402
miles [Thu, 11 Oct 2012 22:18:58 +0000 (22:18 +0000)]
check boxes no longer disappear after they have been checked, the list
of species is static
svn path=/; revision=401
miles [Thu, 11 Oct 2012 22:01:09 +0000 (22:01 +0000)]
check boxes for removing species from the heat map
svn path=/; revision=400
miles [Thu, 11 Oct 2012 20:14:15 +0000 (20:14 +0000)]
species elimination working, must be known before heatmap is generated.
next update hopefully will have checkboxes.
`
svn path=/; revision=399
preecej [Wed, 10 Oct 2012 23:10:35 +0000 (23:10 +0000)]
Trac #197 and 282
svn path=/; revision=398
preecej [Tue, 9 Oct 2012 21:22:04 +0000 (21:22 +0000)]
Removing old copy of SIA project. "Annotation" is the correct project.
svn path=/; revision=397
preecej [Mon, 8 Oct 2012 19:03:41 +0000 (19:03 +0000)]
Added note about required internet connection
svn path=/; revision=396
preecej [Fri, 5 Oct 2012 19:36:20 +0000 (19:36 +0000)]
svn path=/; revision=395
preecej [Fri, 5 Oct 2012 19:34:32 +0000 (19:34 +0000)]
Changed "apply markup now" icon to running man (avoids conflicts w/ the "Form segment" gears icon), more help doc revisions
svn path=/; revision=394
preecej [Fri, 5 Oct 2012 19:26:49 +0000 (19:26 +0000)]
text revisions
svn path=/; revision=393
preecej [Fri, 5 Oct 2012 19:24:36 +0000 (19:24 +0000)]
Revised help doc. Added "beta" to app name.
svn path=/; revision=392
preecej [Fri, 5 Oct 2012 00:36:52 +0000 (00:36 +0000)]
Help URLs revised.
svn path=/; revision=391
preecej [Fri, 5 Oct 2012 00:36:01 +0000 (00:36 +0000)]
Started revisions on the help doc, pointed at a new helpURL location, and revised wording on the SaveReminder dialog.
svn path=/; revision=390
preecej [Thu, 4 Oct 2012 21:33:40 +0000 (21:33 +0000)]
Revised the clearing of the curator, species, and term selection combo boxes in resetView()
svn path=/; revision=389
preecej [Thu, 4 Oct 2012 19:38:32 +0000 (19:38 +0000)]
Close and Save Reminder f(x) implemented.
svn path=/; revision=388
preecej [Thu, 4 Oct 2012 00:59:25 +0000 (00:59 +0000)]
Tested the Close action. Drafted the Close dialog.
Save action from Close action works, but only when hard-wired.
Next: Return user choice from SaveReminder dialog to Close action.
svn path=/; revision=387
preecej [Tue, 2 Oct 2012 23:49:22 +0000 (23:49 +0000)]
Close Action progress. Now just need to build Close action dialog and trigger Save action when requested.
svn path=/; revision=386
preecej [Tue, 2 Oct 2012 18:46:38 +0000 (18:46 +0000)]
Comment clean-up, changed "Command-W" to "Ctrl-W" on Windows actions.props
svn path=/; revision=385
preecej [Tue, 2 Oct 2012 18:33:59 +0000 (18:33 +0000)]
new application icons
svn path=/; revision=384
preecej [Tue, 2 Oct 2012 17:31:56 +0000 (17:31 +0000)]
Updated image for About dialog
svn path=/; revision=383
preecej [Tue, 2 Oct 2012 00:57:28 +0000 (00:57 +0000)]
Added OS license text and image to About dialog.
svn path=/; revision=382
preecej [Tue, 2 Oct 2012 00:56:38 +0000 (00:56 +0000)]
License image for open source software designation.
svn path=/; revision=381
preecej [Fri, 28 Sep 2012 22:07:40 +0000 (22:07 +0000)]
Added a folder to contain the Plant Reactome project and a subfolder for
the rice reactome curation data (pathways, etc.)
svn path=/; revision=380
preecej [Fri, 28 Sep 2012 19:22:02 +0000 (19:22 +0000)]
test svn commits
svn path=/; revision=379
preecej [Tue, 18 Sep 2012 17:14:51 +0000 (17:14 +0000)]
Two tickets in progress: Trac #149, 188.
Save and Close not done yet.
Object clearing associated with file-switching is improved, but not complete.
svn path=/; revision=378
ahmedi [Mon, 27 Aug 2012 19:24:59 +0000 (19:24 +0000)]
Test commit
svn path=/; revision=377
miles [Wed, 15 Aug 2012 19:09:12 +0000 (19:09 +0000)]
Final modifications. Working download link and image generation. Notes
for future: Downloadable image doesn't have special grey and gold
squares representing 0 and 1 genes, respectively. Possibility of
modification later. If the visual effects of the scroll bars on
heatMap.php page becomes an issue, consider surrounding current div tag
with an additional div tag in order to simulate scrolling.
svn path=/; revision=376
elserj [Wed, 15 Aug 2012 17:40:48 +0000 (17:40 +0000)]
Add back code to use the heatchart.java method
svn path=/; revision=375
preecej [Mon, 13 Aug 2012 22:32:23 +0000 (22:32 +0000)]
Changed Kevin McGuinness' affiliation and added a link to the orig software download
svn path=/; revision=374
miles [Mon, 13 Aug 2012 20:07:50 +0000 (20:07 +0000)]
Deleted unneeded files
svn path=/; revision=373
miles [Mon, 13 Aug 2012 20:06:37 +0000 (20:06 +0000)]
Added Web page files
svn path=/; revision=372
miles [Thu, 9 Aug 2012 21:44:35 +0000 (21:44 +0000)]
Updates for web page compatibility.
svn path=/; revision=371
miles [Wed, 25 Jul 2012 20:48:54 +0000 (20:48 +0000)]
Added webpage stuff.
svn path=/; revision=370
elserj [Wed, 25 Jul 2012 20:35:38 +0000 (20:35 +0000)]
Added HeatChart.java and modified it from original jar file to print the species on top. Also added some color and other options to the heatchart drawing.
svn path=/; revision=369
miles [Mon, 23 Jul 2012 22:53:04 +0000 (22:53 +0000)]
Fully operational image generation, independent of JHeatChart libraries.
svn path=/; revision=368
miles [Mon, 23 Jul 2012 22:16:47 +0000 (22:16 +0000)]
Working copy with JHeatChart.java. Puts the species axis at the bottom of the graph rather than the top.
svn path=/; revision=367
elserj [Fri, 20 Jul 2012 23:37:26 +0000 (23:37 +0000)]
Fixed empty args error. Also added code to print actual SQL error messages
svn path=/; revision=366
miles [Thu, 19 Jul 2012 21:02:54 +0000 (21:02 +0000)]
Tab Delimited File option fully functional. See tmp.txt for an example output file.
svn path=/; revision=365
preecej [Wed, 18 Jul 2012 02:52:09 +0000 (02:52 +0000)]
Added TO (Trait Ontology) web service and db access, fixed Annotation
form bug on listing Publications (no more tilde wildcards.)
svn path=/; revision=364
miles [Tue, 17 Jul 2012 18:38:39 +0000 (18:38 +0000)]
Now able to handle more than one gene at a time.
svn path=/; revision=363
miles [Tue, 17 Jul 2012 18:11:08 +0000 (18:11 +0000)]
Species now unique and alphabetized, geneMaps properly constructed, no errors.
svn path=/; revision=362
miles [Tue, 17 Jul 2012 17:15:11 +0000 (17:15 +0000)]
Trying to move most of workload from java to sql. Hoping to also overcome issues with repeat species in the final list and parsing of data into heatmap format.
svn path=/; revision=361
miles [Mon, 16 Jul 2012 22:14:15 +0000 (22:14 +0000)]
Initial import.
svn path=/; revision=360
preecej [Sat, 14 Jul 2012 00:33:57 +0000 (00:33 +0000)]
Fixed curr_ontology_type bug in transform_gaf, correctly switches
between ontologies in the same file during XML generation
svn path=/; revision=359
preecej [Fri, 13 Jul 2012 17:46:16 +0000 (17:46 +0000)]
Added "Assigned By" field
svn path=/; revision=358
preecej [Fri, 13 Jul 2012 17:25:58 +0000 (17:25 +0000)]
Can now handle "Assigned By" (GAF column 15); fixed a couple of bugs;
added "Vitis vinifera" species handling
svn path=/; revision=357
miles [Mon, 9 Jul 2012 21:13:49 +0000 (21:13 +0000)]
initializing miles van de wetering's file
svn path=/; revision=356
preecej [Sat, 7 Jul 2012 01:33:59 +0000 (01:33 +0000)]
Updated to work for Vitis vinifera (grape) imports. Also handled some
"missing data" scenarios for the Gene Name and Evidence fields.
svn path=/; revision=355
preecej [Fri, 6 Jul 2012 03:24:01 +0000 (03:24 +0000)]
modified to match non-Mac updates to config files
svn path=/; revision=354
preecej [Fri, 6 Jul 2012 00:22:37 +0000 (00:22 +0000)]
Trac #157: closed
#149: still working on recalculating window size and placement for a new image, maybe also need to dispose annotations and segments from previous image.
svn path=/; revision=353
preecej [Wed, 4 Jul 2012 22:29:31 +0000 (22:29 +0000)]
[Trac tickets]
Closed: 204,200,203,202,198
Held: 193,188,186
Working on Trac tickets: 149,157
svn path=/; revision=352
preecej [Wed, 4 Jul 2012 01:56:30 +0000 (01:56 +0000)]
Memory disposal work (when opening a new file) in progress.
svn path=/; revision=351
preecej [Wed, 27 Jun 2012 20:33:34 +0000 (20:33 +0000)]
Changed app name to SIA where necessary, re-added Exit menu option (under File), removed Tools menu dropdown
svn path=/; revision=350
athreyab [Tue, 12 Jun 2012 20:09:20 +0000 (20:09 +0000)]
remove annotated_keyword_listid column
svn path=/; revision=349
athreyab [Mon, 11 Jun 2012 20:13:30 +0000 (20:13 +0000)]
interaction db stuff
svn path=/; revision=348
athreyab [Mon, 11 Jun 2012 20:02:28 +0000 (20:02 +0000)]
renaming image_annotation to image_annotation_db
svn path=/; revision=347
athreyab [Mon, 11 Jun 2012 20:01:00 +0000 (20:01 +0000)]
image annotation database stuff
svn path=/; revision=346
preecej [Thu, 7 Jun 2012 22:05:21 +0000 (22:05 +0000)]
sew together SSR data from 3 different sample transcriptome assemblies
, correlate via BLAST, output SSR count differentials amongst resulting orthologs >
dimer
svn path=/; revision=345
preecej [Wed, 6 Jun 2012 22:57:35 +0000 (22:57 +0000)]
svn path=/; revision=344
athreyab [Tue, 5 Jun 2012 23:35:32 +0000 (23:35 +0000)]
documentation
svn path=/; revision=343
lingutln [Tue, 5 Jun 2012 20:53:56 +0000 (20:53 +0000)]
Coordinates saving functionality and some UI alignments. Done by Nikhil.
svn path=/; revision=342
lingutln [Thu, 31 May 2012 20:45:20 +0000 (20:45 +0000)]
Saving annotated images functionality and UI changes. Done by Nikhil.
svn path=/; revision=341
lingutln [Thu, 31 May 2012 19:34:56 +0000 (19:34 +0000)]
Data storage functionality completed. Done by Nikhil.
svn path=/; revision=340
preecej [Thu, 31 May 2012 19:12:13 +0000 (19:12 +0000)]
Added parameters to the term search web service call for prioritizing exact match and grouping branches
svn path=/; revision=339
preecej [Sat, 26 May 2012 01:38:17 +0000 (01:38 +0000)]
term detail web service fix, and some temp URL testing of the next web service version
svn path=/; revision=338
projects / old-jaiswallab-svn / .git / log