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athreyab [Tue, 1 May 2012 02:36:13 +0000 (02:36 +0000)]
pair/singleton script update
svn path=/; revision=327
athreyab [Tue, 1 May 2012 00:20:22 +0000 (00:20 +0000)]
bash script for creating singleton/pair
svn path=/; revision=326
athreyab [Mon, 16 Apr 2012 20:47:29 +0000 (20:47 +0000)]
illumina parse scripts
svn path=/; revision=325
preecej [Thu, 12 Apr 2012 19:13:58 +0000 (19:13 +0000)]
Changed PO web service term_search URL: removed branch filter
svn path=/; revision=324
preecej [Wed, 11 Apr 2012 23:42:19 +0000 (23:42 +0000)]
Moved permanently to /plantontology repo (/html/services/)
svn path=/; revision=323
preecej [Wed, 11 Apr 2012 23:09:50 +0000 (23:09 +0000)]
changed PO aspect (branch) reference to
"plant_structure_development_stage"
svn path=/; revision=322
preecej [Wed, 11 Apr 2012 22:59:50 +0000 (22:59 +0000)]
Made this service environment-independent. Now refers to db connection
string values with generic names.
svn path=/; revision=321
preecej [Wed, 11 Apr 2012 20:41:51 +0000 (20:41 +0000)]
Updated "plant growth and development stage" to "plant structure
development stage"
svn path=/; revision=320
lingutln [Tue, 10 Apr 2012 20:49:54 +0000 (20:49 +0000)]
Resolved refactoring of segment label. Done by Nikhil.
svn path=/; revision=319
lingutln [Mon, 9 Apr 2012 23:21:19 +0000 (23:21 +0000)]
svn path=/; revision=318
lingutln [Mon, 9 Apr 2012 23:05:07 +0000 (23:05 +0000)]
Base64 Decoding for UBio webservice. Done by Nikhil.
svn path=/; revision=317
lingutln [Mon, 9 Apr 2012 21:05:21 +0000 (21:05 +0000)]
Implemented Ubio Web service integration.(yet to complete reloading functionality) Done by Nikhil.
svn path=/; revision=316
preecej [Wed, 4 Apr 2012 23:53:59 +0000 (23:53 +0000)]
Adding an html_mocks folder for design mocks, first set of content for
PO Image Annotation popup
svn path=/; revision=315
elserj [Wed, 14 Mar 2012 22:20:44 +0000 (22:20 +0000)]
Fix broken relative link with absolute link. Relative would be better but because of the structure of drupal, absolute is required
svn path=/; revision=314
preecej [Tue, 13 Mar 2012 20:39:00 +0000 (20:39 +0000)]
Limited "Recent blog posts" retrieval to 5 lines.
svn path=/; revision=313
preecej [Tue, 13 Mar 2012 20:38:07 +0000 (20:38 +0000)]
New directory used to hold small changes to Drupal basecode. If large
changes start to pile up, consider moving to a complete SVN repo of our
Drupal install.
svn path=/; revision=312
preecej [Mon, 12 Mar 2012 23:21:01 +0000 (23:21 +0000)]
added bullets to right nav blog posts (class item-list)
svn path=/; revision=311
lingutln [Mon, 12 Mar 2012 18:56:49 +0000 (18:56 +0000)]
Latest Commits. Done by Nikhil.
svn path=/; revision=310
preecej [Wed, 7 Mar 2012 22:02:01 +0000 (22:02 +0000)]
stylesheet adjustment for transparent banner background
svn path=/; revision=309
preecej [Wed, 7 Mar 2012 21:30:05 +0000 (21:30 +0000)]
made banner background match general background; should move to new style in CSS
svn path=/; revision=308
preecej [Wed, 7 Mar 2012 21:15:03 +0000 (21:15 +0000)]
Modified DRUPAL HEADER to use Jaiswal Lab logo if no $site_name is provided; need to eventually make this a configurable setting via osu_confident.info
svn path=/; revision=307
lingutln [Mon, 5 Mar 2012 21:08:08 +0000 (21:08 +0000)]
Saving as a zip file functionality. Done by Nikhil.
svn path=/; revision=306
lingutln [Mon, 5 Mar 2012 18:55:24 +0000 (18:55 +0000)]
Saving as a zip functionality. Done by Nikhil.
svn path=/; revision=305
lingutln [Thu, 1 Mar 2012 00:23:54 +0000 (00:23 +0000)]
Saving imagemap as a zip file functionality. Done by Nikhil.
svn path=/; revision=304
athreyab [Tue, 28 Feb 2012 22:44:18 +0000 (22:44 +0000)]
committing missed files and minor changes to the sif script
svn path=/; revision=303
athreyab [Tue, 28 Feb 2012 19:13:12 +0000 (19:13 +0000)]
modifications to add date and column type changes
svn path=/; revision=302
lingutln [Mon, 20 Feb 2012 20:05:09 +0000 (20:05 +0000)]
Minor alignments in Linux and Windows OS. Done by Nikhil.
svn path=/; revision=301
lingutln [Sun, 19 Feb 2012 01:19:09 +0000 (01:19 +0000)]
Minor alignments in Windows machine. Done by Nikhil.
svn path=/; revision=300
lingutln [Sat, 18 Feb 2012 22:49:37 +0000 (22:49 +0000)]
Latest Changes. Done by Nikhil.
svn path=/; revision=299
lingutln [Fri, 10 Feb 2012 21:54:14 +0000 (21:54 +0000)]
Saving metadata to HTML imagemap. Done by Nikhil.
svn path=/; revision=298
lingutln [Fri, 10 Feb 2012 02:46:16 +0000 (02:46 +0000)]
svn path=/; revision=297
preecej [Tue, 7 Feb 2012 01:32:27 +0000 (01:32 +0000)]
Changed curator names in application.properties; added SelectionListener to term lookup combobox
svn path=/; revision=296
lingutln [Mon, 6 Feb 2012 22:25:11 +0000 (22:25 +0000)]
Right panel elements added. Done by Nikhil.
svn path=/; revision=295
preecej [Fri, 3 Feb 2012 23:47:46 +0000 (23:47 +0000)]
Corrected relative path of rotating images gallery when no custom path
provided
svn path=/; revision=294
preecej [Thu, 2 Feb 2012 21:23:36 +0000 (21:23 +0000)]
New themes for the Jaiswal Lab site, provided by OSU CWS in Jan 2012.
Not dependent on CWS, will branch and modify/debug locally only as
needed. Note: Standard and Confident themes each have dependencies on OSU
Drupal 1_11 theme. All must be present in Drupal instance for proper
operation.
svn path=/; revision=293
lingutln [Wed, 1 Feb 2012 23:47:37 +0000 (23:47 +0000)]
Added two fields and alignments to the right panel. Done by Nikhil.
svn path=/; revision=292
preecej [Tue, 31 Jan 2012 23:25:19 +0000 (23:25 +0000)]
Refactored web service response term data into Term object. Created Term class; now used by term lookup dropdown and "term edit" popup dialogue. Should also be added to term label, term detail web service response and file metadata export.
svn path=/; revision=291
athreyab [Tue, 31 Jan 2012 22:56:55 +0000 (22:56 +0000)]
allow sif file to be a source of gene information
svn path=/; revision=290
lingutln [Tue, 31 Jan 2012 21:56:32 +0000 (21:56 +0000)]
Right panel modifications. Done by Nikhil.
svn path=/; revision=289
preecej [Tue, 31 Jan 2012 01:33:35 +0000 (01:33 +0000)]
updated list of termDetailTable items to build from an enum (up in declarations)
svn path=/; revision=288
preecej [Tue, 31 Jan 2012 00:09:44 +0000 (00:09 +0000)]
Moved PO web service calls to application.properties file; added lookup label focus listener for PO term details call
svn path=/; revision=287
athreyab [Mon, 30 Jan 2012 22:04:22 +0000 (22:04 +0000)]
removed sample data files and other unwanted script files
svn path=/; revision=286
elserj [Mon, 30 Jan 2012 21:46:02 +0000 (21:46 +0000)]
Updated for newer version of physcomitrella fasta file
svn path=/; revision=285
lingutln [Mon, 30 Jan 2012 21:23:23 +0000 (21:23 +0000)]
Layout changes. Done by Nikhil.
svn path=/; revision=284
lingutln [Mon, 30 Jan 2012 00:03:11 +0000 (00:03 +0000)]
ImageMap functionality for multiple labels. Done by Nikhil.
svn path=/; revision=283
athreyab [Sun, 29 Jan 2012 19:11:02 +0000 (19:11 +0000)]
support for looking up existing species information
svn path=/; revision=282
preecej [Thu, 26 Jan 2012 23:50:30 +0000 (23:50 +0000)]
Stubbed out termDetailTable control on the right panel
svn path=/; revision=281
lingutln [Thu, 26 Jan 2012 19:42:18 +0000 (19:42 +0000)]
Multi segment saving to imagemaps (partially done). Done by Nikhil.
svn path=/; revision=280
athreyab [Thu, 26 Jan 2012 01:50:36 +0000 (01:50 +0000)]
addressed a few review comments from Justin
svn path=/; revision=279
elserj [Thu, 26 Jan 2012 00:11:32 +0000 (00:11 +0000)]
Add Venn diagram creation program to svn
svn path=/; revision=278
preecej [Wed, 25 Jan 2012 22:34:24 +0000 (22:34 +0000)]
Renamed bar3 (toolbar 3) to termLookupBar, added accessionId attribute to SegmentationMask, parsed term accession id from lookup service and populated accessionId
svn path=/; revision=277
elserj [Wed, 25 Jan 2012 00:20:51 +0000 (00:20 +0000)]
Added dbconnect_auto subroutine to allow for db connection with supplied credentials, instead of asking for them. Take care to only use in case of pulling credentials from external file (not in svn)
svn path=/; revision=276
lingutln [Tue, 24 Jan 2012 22:14:41 +0000 (22:14 +0000)]
Regular commits. Done by Nikhil.
svn path=/; revision=275
athreyab [Tue, 24 Jan 2012 19:51:05 +0000 (19:51 +0000)]
added a few comments and support to check if the interaction already in tsv script
svn path=/; revision=274
athreyab [Tue, 24 Jan 2012 19:04:36 +0000 (19:04 +0000)]
fixed the accession_right_id issue.
svn path=/; revision=273
lingutln [Mon, 23 Jan 2012 23:07:57 +0000 (23:07 +0000)]
Image map for single segment.Done by Nikhil.
svn path=/; revision=272
lingutln [Mon, 23 Jan 2012 19:10:55 +0000 (19:10 +0000)]
Multiple segmentation and labelling. Done by Nikhil.
svn path=/; revision=271
athreyab [Mon, 23 Jan 2012 01:29:52 +0000 (01:29 +0000)]
modified interaction.pl to suit both sif and tsv format
svn path=/; revision=270
athreyab [Mon, 23 Jan 2012 00:03:16 +0000 (00:03 +0000)]
Removing unwanted files
svn path=/; revision=269
athreyab [Mon, 23 Jan 2012 00:00:18 +0000 (00:00 +0000)]
more changes
svn path=/; revision=268
lingutln [Sat, 21 Jan 2012 02:41:15 +0000 (02:41 +0000)]
Colors for segments and single segment labelling. Done by Nikhil.
svn path=/; revision=267
lingutln [Fri, 20 Jan 2012 19:10:50 +0000 (19:10 +0000)]
Latest commits.Done by Nikhil.
svn path=/; revision=266
lingutln [Wed, 18 Jan 2012 23:06:36 +0000 (23:06 +0000)]
Border combined with segment. Done by Nikhil.
svn path=/; revision=265
lingutln [Tue, 17 Jan 2012 23:27:54 +0000 (23:27 +0000)]
Labeling independent segments. Done by Nikhil.
svn path=/; revision=264
lingutln [Sat, 14 Jan 2012 00:40:47 +0000 (00:40 +0000)]
Working functionality for Layered segmentation. Done by Nikhil.
svn path=/; revision=263
lingutln [Thu, 12 Jan 2012 23:40:35 +0000 (23:40 +0000)]
Separated out the SegmentationObject from SegmentationMask. Done by Nikhil.
svn path=/; revision=262
lingutln [Wed, 11 Jan 2012 23:14:15 +0000 (23:14 +0000)]
Independent segment enabling functionality. Done by Nikhil.
svn path=/; revision=261
lingutln [Tue, 10 Jan 2012 23:39:29 +0000 (23:39 +0000)]
Labeling mode functionality(left click). Done by Nikhil.
svn path=/; revision=260
athreyab [Tue, 10 Jan 2012 18:15:15 +0000 (18:15 +0000)]
interaction path- initial commit
svn path=/; revision=259
lingutln [Tue, 10 Jan 2012 00:13:45 +0000 (00:13 +0000)]
Layered Segmentation. Done by Nikhil.
svn path=/; revision=258
lingutln [Mon, 9 Jan 2012 23:35:10 +0000 (23:35 +0000)]
Layered Segmentation. Done by Nikhil.
svn path=/; revision=257
lingutln [Mon, 9 Jan 2012 02:35:50 +0000 (02:35 +0000)]
Layered Segmentation. Done by Nikhil.
svn path=/; revision=256
preecej [Sat, 7 Jan 2012 02:11:07 +0000 (02:11 +0000)]
Fixed white-box paralogy bug (caused to even-numbered max paralogs);
cleanly separated heat-map f(x) from custom BoxColor; spread heat-map
increments more evenly across the gradient via fixed outer bounds
svn path=/; revision=255
elserj [Fri, 6 Jan 2012 18:14:16 +0000 (18:14 +0000)]
Update to spelled out names, and fix if translation already in file
svn path=/; revision=254
lingutln [Thu, 5 Jan 2012 19:57:09 +0000 (19:57 +0000)]
svn path=/; revision=253
lingutln [Thu, 5 Jan 2012 09:06:11 +0000 (09:06 +0000)]
svn path=/; revision=252
lingutln [Thu, 5 Jan 2012 07:53:37 +0000 (07:53 +0000)]
svn path=/; revision=251
lingutln [Wed, 4 Jan 2012 20:50:36 +0000 (20:50 +0000)]
Layered Segmentation related. Done by Nikhil.
svn path=/; revision=250
lingutln [Tue, 3 Jan 2012 23:02:06 +0000 (23:02 +0000)]
Layering of Segments.Done by Nikhil.
svn path=/; revision=249
lingutln [Tue, 3 Jan 2012 20:00:50 +0000 (20:00 +0000)]
Added new icon for specifying to form a segment. Done by Nikhil.
svn path=/; revision=248
lingutln [Tue, 3 Jan 2012 19:34:43 +0000 (19:34 +0000)]
Modified popup Exception. Done by Nikhil.
svn path=/; revision=247
lingutln [Sun, 1 Jan 2012 01:44:50 +0000 (01:44 +0000)]
Modified Layout for popup dialog. Done by Nikhil.
svn path=/; revision=246
lingutln [Fri, 30 Dec 2011 23:01:28 +0000 (23:01 +0000)]
Popup dialog functionality. Done by Nikhil.
svn path=/; revision=245
lingutln [Thu, 29 Dec 2011 22:58:48 +0000 (22:58 +0000)]
UI for pop up label and modified the getLabels functionality for Annotation combo box. Done by Nikhil.
svn path=/; revision=244
lingutln [Wed, 28 Dec 2011 22:51:04 +0000 (22:51 +0000)]
Popup Label functionality. Done by Nikhil.
svn path=/; revision=243
lingutln [Wed, 28 Dec 2011 08:45:55 +0000 (08:45 +0000)]
Pop up listener functionality. Done by Nikhil.
svn path=/; revision=242
lingutln [Tue, 27 Dec 2011 22:58:54 +0000 (22:58 +0000)]
PO:ID instead of parent, Layout change, cursor change and slight modifications. Done by Nikhil.
svn path=/; revision=241
lingutln [Tue, 27 Dec 2011 03:12:35 +0000 (03:12 +0000)]
Layout Modifications. Done by Nikhil.
svn path=/; revision=240
lingutln [Mon, 26 Dec 2011 22:45:33 +0000 (22:45 +0000)]
Toggling between segmentation and labeling functionality. Done by Nikhil.
svn path=/; revision=239
lingutln [Mon, 26 Dec 2011 21:55:51 +0000 (21:55 +0000)]
Done by Nikhil.
svn path=/; revision=238
lingutln [Mon, 26 Dec 2011 03:18:08 +0000 (03:18 +0000)]
Implemented functionality of toggling between Segmentation mode and labelling mode. Done by Nikhil.
svn path=/; revision=237
lingutln [Fri, 23 Dec 2011 21:02:27 +0000 (21:02 +0000)]
Added Toggle Between Segmentation and Labelling icon in the menu bar. Done by Nikhil.
svn path=/; revision=236
lingutln [Fri, 23 Dec 2011 19:15:30 +0000 (19:15 +0000)]
Modified Enable/Disable functionality. Done by Nikhil.
svn path=/; revision=235
lingutln [Thu, 22 Dec 2011 23:30:21 +0000 (23:30 +0000)]
svn path=/; revision=234
lingutln [Thu, 22 Dec 2011 23:27:43 +0000 (23:27 +0000)]
Modifications to Enable/Disable functionality. Done by Nikhil.
svn path=/; revision=233
lingutln [Thu, 22 Dec 2011 22:26:25 +0000 (22:26 +0000)]
Down arrow functionality for annotation combo box. Done by Nikhil.
svn path=/; revision=232
lingutln [Tue, 20 Dec 2011 22:58:34 +0000 (22:58 +0000)]
svn path=/; revision=231
preecej [Mon, 19 Dec 2011 21:29:45 +0000 (21:29 +0000)]
svn path=/; revision=230
preecej [Mon, 19 Dec 2011 21:29:21 +0000 (21:29 +0000)]
Added to hold jar's assoc. w/ project
svn path=/; revision=229
lingutln [Mon, 19 Dec 2011 19:00:19 +0000 (19:00 +0000)]
Modifications, done by Nikhil.
svn path=/; revision=228
projects / old-jaiswallab-svn / .git / log