jalview.git
14 years agoadded google analytics, updated version.
jprocter [Sun, 13 Jun 2010 14:41:34 +0000 (14:41 +0000)]
added google analytics, updated version.

14 years agodocumented the -colour command line argument.
jprocter [Sat, 12 Jun 2010 12:45:49 +0000 (12:45 +0000)]
documented the -colour command line argument.

14 years agostockholm added as readable format (Lauren Lui commit)
jprocter [Fri, 11 Jun 2010 15:06:15 +0000 (15:06 +0000)]
stockholm added as readable format (Lauren Lui commit)

14 years agoensure enfin service is started in background when desktop is displayed
jprocter [Fri, 11 Jun 2010 14:56:39 +0000 (14:56 +0000)]
ensure enfin service is started in background when desktop is displayed

14 years agojalview 2.5.1 release notes
jprocter [Fri, 11 Jun 2010 14:39:02 +0000 (14:39 +0000)]
jalview 2.5.1 release notes

14 years agopatch for JAL-556 - more robust mapping of sequence to structure sequence with correc...
jprocter [Fri, 11 Jun 2010 09:41:29 +0000 (09:41 +0000)]
patch for JAL-556 - more robust mapping of sequence to structure sequence with correct substitution matrix

14 years agopatch for JAL-556
jprocter [Fri, 11 Jun 2010 09:40:43 +0000 (09:40 +0000)]
patch for JAL-556

14 years agopatched for JAL-531 - only display full symbol distribution stats on tooltip/annotati...
jprocter [Fri, 11 Jun 2010 07:59:41 +0000 (07:59 +0000)]
patched for JAL-531 - only display full symbol distribution stats on tooltip/annotation label when the sequenceLogo is displayed.

14 years agopatch for JAL-545 - make deep copy of feature settings
jprocter [Wed, 9 Jun 2010 14:06:03 +0000 (14:06 +0000)]
patch for JAL-545 - make deep copy of feature settings

14 years agopatch for JAL-555
jprocter [Wed, 9 Jun 2010 12:09:59 +0000 (12:09 +0000)]
patch for JAL-555

14 years agopaste menu display on OSX Leopard * JAL-557
jprocter [Wed, 9 Jun 2010 12:09:08 +0000 (12:09 +0000)]
paste menu display on OSX Leopard * JAL-557

14 years agoOSX look and feel JAL-577
jprocter [Wed, 9 Jun 2010 12:07:58 +0000 (12:07 +0000)]
OSX look and feel JAL-577

14 years agofollowSelections flag now set via user preferences, and disabled for 2.5.1 * JAL...
jprocter [Tue, 8 Jun 2010 14:48:25 +0000 (14:48 +0000)]
followSelections flag now set via user preferences, and disabled for 2.5.1 * JAL-574 and * JAL-576

14 years agobetter test for when to update column selection when receiving a selection message...
jprocter [Tue, 8 Jun 2010 14:30:37 +0000 (14:30 +0000)]
better test for when to update column selection when receiving a selection message * JAL-574

14 years agotrim hidden regions outside selection when copying selected region to clipboard ...
jprocter [Tue, 8 Jun 2010 14:27:25 +0000 (14:27 +0000)]
trim hidden regions outside selection when copying selected region to clipboard * JAL-573

14 years agoPatch for incorrect column selection when hidden regions are present * JAL-558
jprocter [Tue, 8 Jun 2010 14:25:36 +0000 (14:25 +0000)]
Patch for incorrect column selection when hidden regions are present * JAL-558

14 years agoprevent multiple attempts to initialise logging
jprocter [Sun, 6 Jun 2010 14:57:59 +0000 (14:57 +0000)]
prevent multiple attempts to initialise logging

14 years agopatch for JAL-542
jprocter [Sun, 6 Jun 2010 14:57:31 +0000 (14:57 +0000)]
patch for JAL-542

14 years agoFix for * JAL-541
jprocter [Sun, 6 Jun 2010 14:27:51 +0000 (14:27 +0000)]
Fix for * JAL-541

14 years agoresolution for * JAL-553
jprocter [Fri, 4 Jun 2010 16:18:53 +0000 (16:18 +0000)]
resolution for * JAL-553

14 years agoupdate group annotation for new treegroups (JAL-552)
jprocter [Fri, 4 Jun 2010 16:09:48 +0000 (16:09 +0000)]
update group annotation for new treegroups (JAL-552)

14 years agocorrect popup menu, ensure panel doesn't disappear when empty (patches for JAL-554...
jprocter [Fri, 4 Jun 2010 15:45:43 +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)

14 years agofirst patch for JAL-563 - attempt to relayout annotation panel after adjusting heights
jprocter [Fri, 4 Jun 2010 15:44:15 +0000 (15:44 +0000)]
first patch for JAL-563 - attempt to relayout annotation panel after adjusting heights

14 years agopatches for JAL-554 and JAL-570
jprocter [Fri, 4 Jun 2010 15:40:32 +0000 (15:40 +0000)]
patches for JAL-554 and JAL-570
focus is explicitly handed back to caller (JAL-566)

14 years agofocus is explicitly handed back to caller (JAL-566)
jprocter [Fri, 4 Jun 2010 15:40:19 +0000 (15:40 +0000)]
focus is explicitly handed back to caller (JAL-566)

14 years agoensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL...
jprocter [Fri, 4 Jun 2010 15:39:44 +0000 (15:39 +0000)]
ensure panel doesn't disappear when empty (patches for JAL-554 and JAL-570 and JAL-562)

14 years agopatch re JAL-554
jprocter [Thu, 3 Jun 2010 15:14:16 +0000 (15:14 +0000)]
patch re JAL-554

14 years agopatch ensuring annotation is output correctly re * JAL-554
jprocter [Thu, 3 Jun 2010 15:13:49 +0000 (15:13 +0000)]
patch ensuring annotation is output correctly re * JAL-554

14 years agopatch and error reports re JAL-554
jprocter [Thu, 3 Jun 2010 15:12:42 +0000 (15:12 +0000)]
patch and error reports re JAL-554

14 years agojavadoc re JAL-554
jprocter [Thu, 3 Jun 2010 15:12:20 +0000 (15:12 +0000)]
javadoc re  JAL-554

14 years agopatches for # JAL-254 and JAL-548
jprocter [Tue, 1 Jun 2010 11:28:57 +0000 (11:28 +0000)]
patches for # JAL-254 and JAL-548

14 years agoremoved vamsas deps
jprocter [Tue, 1 Jun 2010 09:06:29 +0000 (09:06 +0000)]
removed vamsas deps

14 years agoquick workaround for JAL-537.
jprocter [Fri, 21 May 2010 09:43:24 +0000 (09:43 +0000)]
quick workaround for JAL-537.

14 years agopartial patch for * JAL-466
jprocter [Fri, 14 May 2010 14:37:23 +0000 (14:37 +0000)]
partial patch for * JAL-466
allows finder to be instantiated for an explicit alignment panel and viewport.

14 years agopartial patch for * JAL-466
jprocter [Fri, 14 May 2010 14:34:06 +0000 (14:34 +0000)]
partial patch for * JAL-466
allows finder to be instantiated for an explicit alignment panel and viewport.

14 years agofix for JAL-533
jprocter [Fri, 14 May 2010 11:47:38 +0000 (11:47 +0000)]
fix for JAL-533

14 years agopatch for JAL-528
jprocter [Wed, 12 May 2010 09:36:39 +0000 (09:36 +0000)]
patch for JAL-528

14 years agofix for JAL-527
jprocter [Wed, 12 May 2010 08:46:30 +0000 (08:46 +0000)]
fix for JAL-527

14 years agojalview 2.5 documentation (still)
jprocter [Sat, 1 May 2010 17:29:14 +0000 (17:29 +0000)]
jalview 2.5 documentation (still)

14 years agocorrect branch
jprocter [Sat, 1 May 2010 16:17:40 +0000 (16:17 +0000)]
correct branch

14 years agorelocatable reference to build file and dropped groovy library from classpath Root_Release_2_5_Branch
jprocter [Sat, 1 May 2010 15:40:30 +0000 (15:40 +0000)]
relocatable reference to build file and dropped groovy library from classpath

14 years agohref for version
jprocter [Sat, 1 May 2010 15:25:29 +0000 (15:25 +0000)]
href for version

14 years ago2.5 release details Release_2_5 Release_2_5_branch
jprocter [Fri, 30 Apr 2010 16:05:04 +0000 (16:05 +0000)]
2.5 release details

14 years ago2.5 release notes
jprocter [Fri, 30 Apr 2010 15:51:33 +0000 (15:51 +0000)]
2.5 release notes

14 years agoget the html header comment right!
jprocter [Fri, 30 Apr 2010 15:11:37 +0000 (15:11 +0000)]
get the html header comment right!

14 years agoget the html header comment right!
jprocter [Fri, 30 Apr 2010 14:11:06 +0000 (14:11 +0000)]
get the html header comment right!

14 years agotidying for 2.5 release
jprocter [Fri, 30 Apr 2010 14:10:29 +0000 (14:10 +0000)]
tidying for 2.5 release

14 years agopatch for bug #59999
jprocter [Fri, 30 Apr 2010 13:19:37 +0000 (13:19 +0000)]
patch for bug #59999

14 years agodoc
jprocter [Fri, 30 Apr 2010 11:52:50 +0000 (11:52 +0000)]
doc

14 years agosort by length
jprocter [Fri, 30 Apr 2010 11:52:23 +0000 (11:52 +0000)]
sort by length

14 years agojalview 2.5 release banner
jprocter [Fri, 30 Apr 2010 09:39:12 +0000 (09:39 +0000)]
jalview 2.5 release banner

14 years agojalview 2.5 release banner
jprocter [Fri, 30 Apr 2010 09:30:38 +0000 (09:30 +0000)]
jalview 2.5 release banner

14 years agoclasspath for eclipse is shared
jprocter [Fri, 30 Apr 2010 09:16:48 +0000 (09:16 +0000)]
classpath for eclipse is shared

14 years ago2.5 doc
jprocter [Fri, 30 Apr 2010 07:03:41 +0000 (07:03 +0000)]
2.5 doc

14 years ago2.5 hidden capabilities
jprocter [Fri, 30 Apr 2010 07:02:49 +0000 (07:02 +0000)]
2.5 hidden capabilities

14 years agovamsas 0.2 client capabilities
jprocter [Fri, 30 Apr 2010 07:02:32 +0000 (07:02 +0000)]
vamsas 0.2 client capabilities

14 years agomake sure references are intact when group annotation is accessed
jprocter [Thu, 29 Apr 2010 16:09:07 +0000 (16:09 +0000)]
make sure references are intact when group annotation is accessed

14 years agohighlighting/selecting is application only for 2.5.0 release
jprocter [Thu, 29 Apr 2010 15:12:10 +0000 (15:12 +0000)]
highlighting/selecting is application only for 2.5.0 release

14 years ago2.5 release doc
jprocter [Thu, 29 Apr 2010 15:03:44 +0000 (15:03 +0000)]
2.5 release doc

14 years agoisAligned assertion (bug 0008144)
jprocter [Thu, 29 Apr 2010 15:03:07 +0000 (15:03 +0000)]
isAligned assertion (bug 0008144)

14 years agoproperty change race condition (bug 0062693) and 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)

14 years agohide/show selected region menu entries and key bindings
jprocter [Thu, 29 Apr 2010 11:13:01 +0000 (11:13 +0000)]
hide/show selected region menu entries and key bindings

14 years agonew selection manipulation method
jprocter [Thu, 29 Apr 2010 11:12:16 +0000 (11:12 +0000)]
new selection manipulation method

14 years agopopup menu toggles between graduated colour and single colour feature style
jprocter [Thu, 29 Apr 2010 08:51:30 +0000 (08:51 +0000)]
popup menu toggles between graduated colour and single colour feature style

14 years agoosx pixel tweak
jprocter [Thu, 29 Apr 2010 08:50:54 +0000 (08:50 +0000)]
osx pixel tweak

14 years agoeclipse source code formatting
jprocter [Thu, 29 Apr 2010 08:45:48 +0000 (08:45 +0000)]
eclipse source code formatting

14 years agoshare eclipse settings
jprocter [Thu, 29 Apr 2010 08:38:54 +0000 (08:38 +0000)]
share eclipse settings

14 years agojog pixels for OSX
jprocter [Wed, 28 Apr 2010 17:01:27 +0000 (17:01 +0000)]
jog pixels for OSX

14 years agoosx button colouring issue
jprocter [Wed, 28 Apr 2010 17:01:17 +0000 (17:01 +0000)]
osx button colouring issue

14 years agojog pixels for OSX
jprocter [Wed, 28 Apr 2010 14:23:18 +0000 (14:23 +0000)]
jog pixels for OSX

14 years agofind incrementally searches ID then subsequence matches. Dialog reports number of...
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)

14 years agofind incrementally searches ID then subsequence matches.
jprocter [Wed, 28 Apr 2010 14:03:21 +0000 (14:03 +0000)]
find incrementally searches ID then subsequence matches.

14 years agoexcludes
jprocter [Wed, 28 Apr 2010 10:25:44 +0000 (10:25 +0000)]
excludes

14 years agocheck class versions
jprocter [Wed, 28 Apr 2010 10:25:37 +0000 (10:25 +0000)]
check class versions

14 years ago2.5 updates...
jprocter [Wed, 28 Apr 2010 10:23:26 +0000 (10:23 +0000)]
2.5 updates...

14 years agograduated feature schemes
jprocter [Wed, 28 Apr 2010 10:23:07 +0000 (10:23 +0000)]
graduated feature schemes

14 years agotypo
jprocter [Wed, 28 Apr 2010 10:22:37 +0000 (10:22 +0000)]
typo

14 years agoenvision2 service
jprocter [Wed, 28 Apr 2010 10:22:27 +0000 (10:22 +0000)]
envision2 service

14 years agobetter ui description
jprocter [Wed, 28 Apr 2010 10:21:56 +0000 (10:21 +0000)]
better ui description

14 years agomake groups function
jprocter [Wed, 28 Apr 2010 10:21:33 +0000 (10:21 +0000)]
make groups function

14 years agograduated feature schemes (with visual indication of thresholding)
jprocter [Wed, 28 Apr 2010 10:21:20 +0000 (10:21 +0000)]
graduated feature schemes (with visual indication of thresholding)

14 years agogroup/annotation association, logos, autocalc group annotation and sequence id tooltip
jprocter [Wed, 28 Apr 2010 10:21:05 +0000 (10:21 +0000)]
group/annotation association, logos, autocalc group annotation and sequence id tooltip

14 years agonull pointer when double click event occurs without an existing selection (happens...
jprocter [Wed, 28 Apr 2010 10:18:56 +0000 (10:18 +0000)]
null pointer when double click event occurs without an existing selection (happens when tooltip position has been locked using shift key, and then user double clicks).

14 years agomake groups from selection
jprocter [Wed, 28 Apr 2010 10:17:09 +0000 (10:17 +0000)]
make groups from selection

14 years agogroup/annotation association
jprocter [Wed, 28 Apr 2010 10:16:32 +0000 (10:16 +0000)]
group/annotation association

14 years agogroup/annotation association housekeeping
jprocter [Wed, 28 Apr 2010 10:15:51 +0000 (10:15 +0000)]
group/annotation association housekeeping

14 years agonew applet parameters: heightScale and widthScale
jprocter [Mon, 26 Apr 2010 10:00:53 +0000 (10:00 +0000)]
new applet parameters: heightScale and widthScale

14 years agobuild date output in the About box, and build details output on startup when debug...
jprocter [Mon, 26 Apr 2010 09:32:15 +0000 (09:32 +0000)]
build date output in the About box, and build details output on startup when debug flag is set.

14 years agodisabled the justify functions for 2.5 release (see bug # 62495 )
jprocter [Mon, 26 Apr 2010 09:31:33 +0000 (09:31 +0000)]
disabled the justify functions for 2.5 release (see bug # 62495 )

14 years agoupgrade to Vamsas client 0.2
jprocter [Fri, 23 Apr 2010 16:17:00 +0000 (16:17 +0000)]
upgrade to  Vamsas client 0.2

14 years agoskips any annotation that appears to be identical to existing autogenerated annotatio...
jprocter [Fri, 23 Apr 2010 15:59:56 +0000 (15:59 +0000)]
skips any annotation that appears to be identical to existing autogenerated annotation on the alignment.

14 years agonext attempt for Bug #36198 - appears to work reproducibly
jprocter [Fri, 23 Apr 2010 15:11:10 +0000 (15:11 +0000)]
next attempt for Bug #36198 - appears to work reproducibly

14 years agotooltip is not shown for Annotation elements with zero length description
jprocter [Fri, 23 Apr 2010 15:10:22 +0000 (15:10 +0000)]
tooltip is not shown for Annotation elements with zero length description

14 years agojavadoc
jprocter [Fri, 23 Apr 2010 15:09:40 +0000 (15:09 +0000)]
javadoc

14 years agothread off a Filechooser instance on startup to make the dialog open quicker later on.
jprocter [Fri, 23 Apr 2010 14:20:46 +0000 (14:20 +0000)]
thread off a Filechooser instance on startup to make the dialog open quicker later on.

14 years agodefault value boolean parameter getter
jprocter [Fri, 23 Apr 2010 12:20:56 +0000 (12:20 +0000)]
default value boolean parameter getter

14 years agofix for bug #8333
jprocter [Fri, 23 Apr 2010 12:20:42 +0000 (12:20 +0000)]
fix for bug #8333

14 years agofix for bug #62456
jprocter [Fri, 23 Apr 2010 12:19:24 +0000 (12:19 +0000)]
fix for bug #62456

14 years agoported logo rendering and label fit to column width - but disabled due to 1.1 incompa...
jprocter [Fri, 23 Apr 2010 10:56:28 +0000 (10:56 +0000)]
ported logo rendering and label fit to column width - but disabled due to 1.1 incompatibility.

14 years agoported basic elements of logo and group annotation display, but disabled due to 1...
jprocter [Fri, 23 Apr 2010 10:55:31 +0000 (10:55 +0000)]
ported basic elements of logo and group annotation display, but disabled due to 1.1 incompatibility.