jprocter [Mon, 14 Jun 2010 11:21:34 +0000 (11:21 +0000)]
patch for JAL-572
jprocter [Mon, 14 Jun 2010 10:51:48 +0000 (10:51 +0000)]
added min-jws2 jar to classpath
jprocter [Mon, 14 Jun 2010 10:18:04 +0000 (10:18 +0000)]
JGoogleAnalytics on classpath.
jprocter [Sat, 12 Jun 2010 12:45:52 +0000 (12:45 +0000)]
documented the -colour command line argument.
jprocter [Fri, 11 Jun 2010 15:06:12 +0000 (15:06 +0000)]
stockholm added as readable format (Lauren Lui commit)
jprocter [Fri, 11 Jun 2010 14:57:02 +0000 (14:57 +0000)]
ensure enfin service is started in background when desktop is displayed
jprocter [Fri, 11 Jun 2010 14:39:04 +0000 (14:39 +0000)]
jalview 2.5.1 release notes
jprocter [Fri, 11 Jun 2010 09:54:26 +0000 (09:54 +0000)]
patch for JAL-556 - more robust mapping of sequence to structure sequence with correct substitution matrix
jprocter [Fri, 11 Jun 2010 09:54:14 +0000 (09:54 +0000)]
patch for JAL-556
jprocter [Fri, 11 Jun 2010 07:59:54 +0000 (07:59 +0000)]
patched for JAL-531 - only display full symbol distribution stats on tooltip/annotation label when the sequenceLogo is displayed.
jprocter [Wed, 9 Jun 2010 14:06:02 +0000 (14:06 +0000)]
patch for JAL-545 - make deep copy of feature settings
jprocter [Wed, 9 Jun 2010 12:09:58 +0000 (12:09 +0000)]
patch for JAL-555
jprocter [Wed, 9 Jun 2010 12:09:07 +0000 (12:09 +0000)]
paste menu display on OSX Leopard * JAL-557
jprocter [Wed, 9 Jun 2010 12:07:57 +0000 (12:07 +0000)]
OSX look and feel JAL-577
jprocter [Tue, 8 Jun 2010 14:48:29 +0000 (14:48 +0000)]
followSelections flag now set via user preferences, and disabled for 2.5.1 * JAL-574 and * JAL-576
jprocter [Tue, 8 Jun 2010 14:30:34 +0000 (14:30 +0000)]
better test for when to update column selection when receiving a selection message * JAL-574
jprocter [Tue, 8 Jun 2010 14:27:20 +0000 (14:27 +0000)]
trim hidden regions outside selection when copying selected region to clipboard * JAL-573
jprocter [Tue, 8 Jun 2010 14:25:35 +0000 (14:25 +0000)]
Patch for incorrect column selection when hidden regions are present * JAL-558
jprocter [Sun, 6 Jun 2010 14:57:15 +0000 (14:57 +0000)]
patch for JAL-542
jprocter [Sun, 6 Jun 2010 14:27:48 +0000 (14:27 +0000)]
Fix for * JAL-541
jprocter [Fri, 4 Jun 2010 16:18:54 +0000 (16:18 +0000)]
resolution for * JAL-553
jprocter [Fri, 4 Jun 2010 16:09:49 +0000 (16:09 +0000)]
update group annotation for new treegroups (JAL-552)
jprocter [Fri, 4 Jun 2010 15:45:44 +0000 (15:45 +0000)]
correct popup menu, ensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL-562) and first patch for annotation label redraw (JAL-563)
jprocter [Fri, 4 Jun 2010 15:44:14 +0000 (15:44 +0000)]
first patch for JAL-563 - attempt to relayout annotation panel after adjusting heights
jprocter [Fri, 4 Jun 2010 15:39:01 +0000 (15:39 +0000)]
ensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL-562)
jprocter [Fri, 4 Jun 2010 15:32:37 +0000 (15:32 +0000)]
patches for JAL-554 and JAL-570
focus is explicitly handed back to caller (JAL-566)
jprocter [Fri, 4 Jun 2010 15:26:44 +0000 (15:26 +0000)]
focus is explicitly handed back to caller (JAL-566)
jprocter [Fri, 4 Jun 2010 15:20:46 +0000 (15:20 +0000)]
focus is explicitly handed back to caller (JAL-566)
jprocter [Thu, 3 Jun 2010 15:25:03 +0000 (15:25 +0000)]
typo (ahem)
jprocter [Thu, 3 Jun 2010 15:14:15 +0000 (15:14 +0000)]
patch re JAL-554
jprocter [Thu, 3 Jun 2010 15:13:48 +0000 (15:13 +0000)]
patch ensuring annotation is output correctly re * JAL-554
jprocter [Thu, 3 Jun 2010 15:12:41 +0000 (15:12 +0000)]
patch and error reports re JAL-554
jprocter [Thu, 3 Jun 2010 15:12:19 +0000 (15:12 +0000)]
javadoc re JAL-554
jprocter [Thu, 3 Jun 2010 13:59:44 +0000 (13:59 +0000)]
fix and warning message in case the JWS2 jar is not available.
jprocter [Tue, 1 Jun 2010 11:29:30 +0000 (11:29 +0000)]
patches for # JAL-254 and JAL-548
jprocter [Fri, 21 May 2010 10:08:08 +0000 (10:08 +0000)]
more robust discovery and preset support
jprocter [Fri, 21 May 2010 10:07:55 +0000 (10:07 +0000)]
preset and argument support
jprocter [Fri, 21 May 2010 10:07:17 +0000 (10:07 +0000)]
comment about trapping OOMs
jprocter [Fri, 21 May 2010 10:06:56 +0000 (10:06 +0000)]
commented out debug code
jprocter [Fri, 21 May 2010 09:35:49 +0000 (09:35 +0000)]
quick workaround for JAL-537.
jprocter [Mon, 17 May 2010 16:15:12 +0000 (16:15 +0000)]
status can be null to begin with
jprocter [Mon, 17 May 2010 16:14:48 +0000 (16:14 +0000)]
pullJobExecutionStats for JAL-493
jprocter [Mon, 17 May 2010 16:13:36 +0000 (16:13 +0000)]
minor fix for * JAL-537
jprocter [Mon, 17 May 2010 16:13:06 +0000 (16:13 +0000)]
more robust jws2 service discovery
jprocter [Mon, 17 May 2010 16:12:18 +0000 (16:12 +0000)]
refactored old jalview service code to its own package.
jprocter [Mon, 17 May 2010 10:17:14 +0000 (10:17 +0000)]
always pass full web service exception details to the log
jprocter [Mon, 17 May 2010 09:56:31 +0000 (09:56 +0000)]
always pass full web service exception details to the log
jprocter [Mon, 17 May 2010 09:56:06 +0000 (09:56 +0000)]
always log info about services that are discovered
jprocter [Fri, 14 May 2010 17:09:47 +0000 (17:09 +0000)]
First patch for * JAL-493
- bespoke build of the jalview ws2 client library with refactored base client.
jprocter [Fri, 14 May 2010 17:08:57 +0000 (17:08 +0000)]
First patch for * JAL-493
jprocter [Fri, 14 May 2010 17:04:08 +0000 (17:04 +0000)]
standard function for bootstrapping discovery threads
jprocter [Fri, 14 May 2010 17:03:29 +0000 (17:03 +0000)]
allow initLogger to be called multiple times
jprocter [Fri, 14 May 2010 14:37:10 +0000 (14:37 +0000)]
partial patch for * JAL-466
allows finder to be instantiated for an explicit alignment panel and viewport.
jprocter [Fri, 14 May 2010 11:46:12 +0000 (11:46 +0000)]
fix for JAL-533
jprocter [Wed, 12 May 2010 09:37:18 +0000 (09:37 +0000)]
debug comment
jprocter [Wed, 12 May 2010 09:37:10 +0000 (09:37 +0000)]
patch for JAL-528
jprocter [Wed, 12 May 2010 08:38:07 +0000 (08:38 +0000)]
fix for JAL-527
jprocter [Sat, 1 May 2010 17:31:24 +0000 (17:31 +0000)]
jalview 2.5 documentation (still)
jprocter [Sat, 1 May 2010 15:50:16 +0000 (15:50 +0000)]
branched 2.5 version
jprocter [Sat, 1 May 2010 15:40:30 +0000 (15:40 +0000)]
relocatable reference to build file and dropped groovy library from classpath
jprocter [Sat, 1 May 2010 15:25:29 +0000 (15:25 +0000)]
href for version
jprocter [Fri, 30 Apr 2010 16:05:04 +0000 (16:05 +0000)]
2.5 release details
jprocter [Fri, 30 Apr 2010 15:51:33 +0000 (15:51 +0000)]
2.5 release notes
jprocter [Fri, 30 Apr 2010 15:11:37 +0000 (15:11 +0000)]
get the html header comment right!
jprocter [Fri, 30 Apr 2010 14:11:06 +0000 (14:11 +0000)]
get the html header comment right!
jprocter [Fri, 30 Apr 2010 14:10:29 +0000 (14:10 +0000)]
tidying for 2.5 release
jprocter [Fri, 30 Apr 2010 13:19:37 +0000 (13:19 +0000)]
patch for bug #59999
jprocter [Fri, 30 Apr 2010 11:52:50 +0000 (11:52 +0000)]
doc
jprocter [Fri, 30 Apr 2010 11:52:23 +0000 (11:52 +0000)]
sort by length
jprocter [Fri, 30 Apr 2010 09:39:12 +0000 (09:39 +0000)]
jalview 2.5 release banner
jprocter [Fri, 30 Apr 2010 09:30:38 +0000 (09:30 +0000)]
jalview 2.5 release banner
jprocter [Fri, 30 Apr 2010 09:16:48 +0000 (09:16 +0000)]
classpath for eclipse is shared
jprocter [Fri, 30 Apr 2010 07:03:41 +0000 (07:03 +0000)]
2.5 doc
jprocter [Fri, 30 Apr 2010 07:02:49 +0000 (07:02 +0000)]
2.5 hidden capabilities
jprocter [Fri, 30 Apr 2010 07:02:32 +0000 (07:02 +0000)]
vamsas 0.2 client capabilities
jprocter [Thu, 29 Apr 2010 16:09:07 +0000 (16:09 +0000)]
make sure references are intact when group annotation is accessed
jprocter [Thu, 29 Apr 2010 15:12:10 +0000 (15:12 +0000)]
highlighting/selecting is application only for 2.5.0 release
jprocter [Thu, 29 Apr 2010 15:03:44 +0000 (15:03 +0000)]
2.5 release doc
jprocter [Thu, 29 Apr 2010 15:03:07 +0000 (15:03 +0000)]
isAligned assertion (bug 0008144)
jprocter [Thu, 29 Apr 2010 15:02:42 +0000 (15:02 +0000)]
property change race condition (bug 0062693) and isAligned assertion (bug 0008144)
jprocter [Thu, 29 Apr 2010 11:13:01 +0000 (11:13 +0000)]
hide/show selected region menu entries and key bindings
jprocter [Thu, 29 Apr 2010 11:12:16 +0000 (11:12 +0000)]
new selection manipulation method
jprocter [Thu, 29 Apr 2010 08:51:30 +0000 (08:51 +0000)]
popup menu toggles between graduated colour and single colour feature style
jprocter [Thu, 29 Apr 2010 08:50:54 +0000 (08:50 +0000)]
osx pixel tweak
jprocter [Thu, 29 Apr 2010 08:45:48 +0000 (08:45 +0000)]
eclipse source code formatting
jprocter [Thu, 29 Apr 2010 08:38:54 +0000 (08:38 +0000)]
share eclipse settings
jprocter [Wed, 28 Apr 2010 17:01:27 +0000 (17:01 +0000)]
jog pixels for OSX
jprocter [Wed, 28 Apr 2010 17:01:17 +0000 (17:01 +0000)]
osx button colouring issue
jprocter [Wed, 28 Apr 2010 14:23:18 +0000 (14:23 +0000)]
jog pixels for OSX
jprocter [Wed, 28 Apr 2010 14:03:51 +0000 (14:03 +0000)]
find incrementally searches ID then subsequence matches. Dialog reports number of ID and subsequence matches correctly (bugfix)
jprocter [Wed, 28 Apr 2010 14:03:21 +0000 (14:03 +0000)]
find incrementally searches ID then subsequence matches.
jprocter [Wed, 28 Apr 2010 10:25:44 +0000 (10:25 +0000)]
excludes
jprocter [Wed, 28 Apr 2010 10:25:37 +0000 (10:25 +0000)]
check class versions
jprocter [Wed, 28 Apr 2010 10:23:26 +0000 (10:23 +0000)]
2.5 updates...
jprocter [Wed, 28 Apr 2010 10:23:07 +0000 (10:23 +0000)]
graduated feature schemes
jprocter [Wed, 28 Apr 2010 10:22:37 +0000 (10:22 +0000)]
typo
jprocter [Wed, 28 Apr 2010 10:22:27 +0000 (10:22 +0000)]
envision2 service
jprocter [Wed, 28 Apr 2010 10:21:56 +0000 (10:21 +0000)]
better ui description
jprocter [Wed, 28 Apr 2010 10:21:33 +0000 (10:21 +0000)]
make groups function
jprocter [Wed, 28 Apr 2010 10:21:20 +0000 (10:21 +0000)]
graduated feature schemes (with visual indication of thresholding)
git://source.jalview.org / jalview.git / log