jprocter [Sat, 17 Nov 2012 18:47:51 +0000 (18:47 +0000)]
openjdk7 returns null for default value selected format if it hasn't been touched
jprocter [Sat, 17 Nov 2012 18:35:43 +0000 (18:35 +0000)]
method to construct sequence mapping for matching positions in aligned sequences
jprocter [Sat, 17 Nov 2012 18:34:37 +0000 (18:34 +0000)]
convenience method for performing pairwise alignment
jprocter [Sat, 17 Nov 2012 18:33:46 +0000 (18:33 +0000)]
formatting and javadoc
jprocter [Thu, 15 Nov 2012 15:25:22 +0000 (15:25 +0000)]
remove java7 plugin dependency
jprocter [Thu, 15 Nov 2012 15:22:01 +0000 (15:22 +0000)]
don't set background colour for menu bar
jprocter [Thu, 15 Nov 2012 15:21:34 +0000 (15:21 +0000)]
allow .rnaml as a filename extension
jprocter [Thu, 15 Nov 2012 15:19:11 +0000 (15:19 +0000)]
comment on jalview.io.AlignFile architecture
jprocter [Thu, 15 Nov 2012 15:18:29 +0000 (15:18 +0000)]
source formatting
jprocter [Thu, 15 Nov 2012 15:15:04 +0000 (15:15 +0000)]
Merge branch 'develop' into menard
Conflicts:
src/MCview/PDBfile.java
src/jalview/analysis/Rna.java
src/jalview/analysis/StructureFrequency.java
src/jalview/appletgui/AlignFrame.java
src/jalview/datamodel/Sequence.java
src/jalview/ext/varna/VarnaCommands.java
src/jalview/gui/AppVarna.java
src/jalview/gui/AssociatePdbFileWithSeq.java
src/jalview/gui/PopupMenu.java
src/jalview/io/FeaturesFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/renderer/AnnotationRenderer.java
src/jalview/schemes/ColourSchemeProperty.java
src/jalview/schemes/ResidueColourScheme.java
src/jalview/workers/StrucConsensusThread.java
jprocter [Tue, 13 Nov 2012 17:49:01 +0000 (17:49 +0000)]
Merge branch 'master' into develop
jprocter [Mon, 12 Nov 2012 11:36:47 +0000 (11:36 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Mon, 12 Nov 2012 11:36:16 +0000 (11:36 +0000)]
final tweaks to help landing page
jprocter [Mon, 12 Nov 2012 11:12:49 +0000 (11:12 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Mon, 12 Nov 2012 11:10:12 +0000 (11:10 +0000)]
update footer for static page
jprocter [Mon, 12 Nov 2012 10:00:29 +0000 (10:00 +0000)]
Merge branch 'Release_2_8_Branch'
jprocter [Sun, 11 Nov 2012 11:23:11 +0000 (11:23 +0000)]
tidy help
jprocter [Fri, 9 Nov 2012 17:00:09 +0000 (17:00 +0000)]
property to configure webstart image
jprocter [Fri, 9 Nov 2012 16:56:10 +0000 (16:56 +0000)]
tweak file association comment and make sure webstart image is published
jprocter [Fri, 9 Nov 2012 16:35:45 +0000 (16:35 +0000)]
push jalview v2.8 release date to monday 12th November
jprocter [Fri, 9 Nov 2012 16:08:50 +0000 (16:08 +0000)]
ga tracking, footers and footer link styles
jprocter [Fri, 9 Nov 2012 15:32:04 +0000 (15:32 +0000)]
more tweaking of static pages and rejigging applet parameter documentation for accessibility
jprocter [Fri, 9 Nov 2012 14:38:11 +0000 (14:38 +0000)]
tweak whats new again
jprocter [Fri, 9 Nov 2012 13:04:39 +0000 (13:04 +0000)]
tweaking welcome message and what's new
jprocter [Fri, 9 Nov 2012 08:02:00 +0000 (08:02 +0000)]
constructor takes settings from any existing feature renderer on alignment panel
jprocter [Thu, 8 Nov 2012 17:45:43 +0000 (17:45 +0000)]
JAL-1193 ensure the 'loadedComplete' method gets called for all views
after the views have been opened by using the Swing stack as a queue
cruisecontrol [Thu, 8 Nov 2012 16:49:53 +0000 (16:49 +0000)]
update installAnywhere classpath and libs for jalview 2.8
jprocter [Thu, 8 Nov 2012 16:29:30 +0000 (16:29 +0000)]
update release notes for JAL-1202
cruisecontrol [Thu, 8 Nov 2012 16:21:39 +0000 (16:21 +0000)]
JAL-1202 included examples and also added in jdas jars and the groovy library
jprocter [Thu, 8 Nov 2012 15:41:51 +0000 (15:41 +0000)]
remember to close input file!
jprocter [Thu, 8 Nov 2012 15:41:34 +0000 (15:41 +0000)]
tidy imports
jprocter [Thu, 8 Nov 2012 10:59:13 +0000 (10:59 +0000)]
embed links to major features in main page
jprocter [Thu, 8 Nov 2012 10:58:54 +0000 (10:58 +0000)]
tweak wording
jprocter [Wed, 7 Nov 2012 17:28:32 +0000 (17:28 +0000)]
patch broken link
jprocter [Wed, 7 Nov 2012 17:18:20 +0000 (17:18 +0000)]
and more tweaks.
jprocter [Wed, 7 Nov 2012 17:15:08 +0000 (17:15 +0000)]
JAL-1201 more layout tweaks
jprocter [Wed, 7 Nov 2012 17:07:05 +0000 (17:07 +0000)]
JAL-1201 tweak layout for applet page and allow monospace <pre> tags
jprocter [Wed, 7 Nov 2012 15:59:39 +0000 (15:59 +0000)]
JAL-1201 more tweaks to page layout
jprocter [Wed, 7 Nov 2012 15:42:19 +0000 (15:42 +0000)]
Jalview 2.8 release notes and whats new! text
jprocter [Wed, 7 Nov 2012 15:11:58 +0000 (15:11 +0000)]
updated release notes for Jalview Version 2.8
jprocter [Wed, 7 Nov 2012 15:11:16 +0000 (15:11 +0000)]
JAL-1201 update pages to use new website design
jprocter [Wed, 7 Nov 2012 15:04:25 +0000 (15:04 +0000)]
JAL-957 manual update to applet authorlist - need to use authorprops (JAL-1200)
jprocter [Wed, 31 Oct 2012 17:05:58 +0000 (17:05 +0000)]
Merge branch 'Release_2_8_Branch' of https://source.jalview.org/git/jalview into Release_2_8_Branch
jprocter [Wed, 31 Oct 2012 17:04:29 +0000 (17:04 +0000)]
JAL-1130 fix gif palette (arggh!)
cruisecontrol [Tue, 30 Oct 2012 18:06:48 +0000 (18:06 +0000)]
JAL-1197 tweak installer more
cruisecontrol [Tue, 30 Oct 2012 17:51:13 +0000 (17:51 +0000)]
JAL-1197 JAL-1198 migrate to IA2012 and new build VM
jprocter [Tue, 30 Oct 2012 17:22:05 +0000 (17:22 +0000)]
JAL-1130 JAL-1197 nice installer splashscreens and fireworks readable pngs for splashscreens
jprocter [Tue, 30 Oct 2012 16:59:19 +0000 (16:59 +0000)]
Merge branch 'Release_2_8_Branch' of https://source.jalview.org/git/jalview into Release_2_8_Branch
jprocter [Tue, 30 Oct 2012 16:58:32 +0000 (16:58 +0000)]
JAL-1130 fireworks editable huge jalview logo in RGB
jprocter [Tue, 30 Oct 2012 16:30:34 +0000 (16:30 +0000)]
JAL-1130 JAL-1197 update install anywhere installer panel
jprocter [Tue, 30 Oct 2012 16:30:34 +0000 (16:30 +0000)]
JAL-1130 JAL-1197 update install anywhere installer panel
jprocter [Tue, 30 Oct 2012 16:17:18 +0000 (16:17 +0000)]
JAL-1130 updated installAnywhere program logos
jprocter [Tue, 30 Oct 2012 16:16:11 +0000 (16:16 +0000)]
JAL-1130 preserved old installAnywhere installer logo as logo_v2
jprocter [Mon, 29 Oct 2012 10:42:43 +0000 (10:42 +0000)]
JAL-1130 made background transparent for small logo (used for application and window icon on Windows platform)
jprocter [Wed, 24 Oct 2012 16:04:11 +0000 (17:04 +0100)]
JAL-1193 call setLoadingFromArchiveFinished(true) for any new structure views, but only after all windows have been loaded and gathered
jprocter [Wed, 24 Oct 2012 16:00:59 +0000 (17:00 +0100)]
JAL-1193 patch prevents JalviewJmolBinding from handling colourBySequence events until setLoadingFromArchiveFinished(true) called
jprocter [Thu, 4 Oct 2012 16:43:26 +0000 (17:43 +0100)]
Jalview 2.8 Source Header
jprocter [Thu, 4 Oct 2012 16:05:22 +0000 (17:05 +0100)]
Merge branch 'develop' into Release_2_8_Branch
jprocter [Thu, 4 Oct 2012 15:56:41 +0000 (16:56 +0100)]
JAL-636 switch to simple REST interface to dbfetch (//ebi.ac.uk/Tools/webservices/services/dbfetch_rest)
jprocter [Thu, 4 Oct 2012 15:48:12 +0000 (16:48 +0100)]
avoid importing the mapping every time we parse a uniprot record.
jprocter [Thu, 4 Oct 2012 15:12:25 +0000 (16:12 +0100)]
JAL-636 tweak main() based test to allow DAS sources to be excluded from basic SequenceFetcher testing
jprocter [Thu, 4 Oct 2012 15:11:08 +0000 (16:11 +0100)]
JAL-1188 - set the user agent to Jalview Desktop/${VERSION}
jprocter [Thu, 4 Oct 2012 11:58:04 +0000 (12:58 +0100)]
JAL-1064 JAL-671 make sure all buttons are disabled during fetch and renabled after it completes
jprocter [Wed, 3 Oct 2012 10:49:43 +0000 (11:49 +0100)]
formatting
jprocter [Wed, 3 Oct 2012 10:13:36 +0000 (11:13 +0100)]
update release branch to v2.8
jprocter [Wed, 3 Oct 2012 09:48:43 +0000 (10:48 +0100)]
formatting
jprocter [Wed, 3 Oct 2012 09:47:27 +0000 (10:47 +0100)]
JAL-1026 - insert a sensible default for proxy so Jalview doesn't crash out immediatly on launch.
jprocter [Wed, 3 Oct 2012 09:45:50 +0000 (10:45 +0100)]
JAL-1183 JAL-343 - use dialog queue for JABA warning dialog box and use html table formatting so dialog box size is sensible.
JAL-1026 - note about checking proxy settings as well as JABAWS URLs.
jprocter [Tue, 2 Oct 2012 15:42:57 +0000 (16:42 +0100)]
JAL-1185 patch NPE - create new group for subtree on each view
jprocter [Mon, 1 Oct 2012 16:14:41 +0000 (17:14 +0100)]
JAL-1130 JAL-1137 messy hardcoding of author list to fixed height so it is visible - means we will have to increase height when more authors are added.
jprocter [Mon, 1 Oct 2012 16:13:35 +0000 (17:13 +0100)]
JAL-1130 JAL-1139 hardcode preferred height to logo image height
jprocter [Mon, 1 Oct 2012 16:11:42 +0000 (17:11 +0100)]
JAL-1130 more robust loading code and different logos for desktop icon and splashscreen icon
jprocter [Mon, 1 Oct 2012 11:15:10 +0000 (12:15 +0100)]
JAL-1183 dialog thread is only started after the splashscreen goes away
jprocter [Mon, 1 Oct 2012 11:14:18 +0000 (12:14 +0100)]
JAL-1111 dialog flickers whilst example file starts if the desktop is not given as parent
jprocter [Mon, 1 Oct 2012 09:56:21 +0000 (10:56 +0100)]
JAL-1184 apparent deadlock when launching jalview on w7 - attempt to patch
jprocter [Mon, 1 Oct 2012 09:14:02 +0000 (10:14 +0100)]
JAL-1183 showNews adds news discovery and display thread to dialog queue
jprocter [Mon, 1 Oct 2012 09:13:02 +0000 (10:13 +0100)]
JAL-1183 use dialog queue for usage statistics prompt
jprocter [Mon, 1 Oct 2012 09:12:35 +0000 (10:12 +0100)]
JAL-1183 dialog queue
jprocter [Thu, 27 Sep 2012 06:32:57 +0000 (07:32 +0100)]
JAL-1030 patch typo
jprocter [Thu, 27 Sep 2012 06:32:28 +0000 (07:32 +0100)]
JAL-1179 - regression from JAL-1030 patch implicitly treats empty selection as null
jprocter [Tue, 25 Sep 2012 14:26:24 +0000 (15:26 +0100)]
JAL-1031 allow empty selections to pass through to tree builder, which will ignore them!
jprocter [Tue, 25 Sep 2012 14:22:09 +0000 (15:22 +0100)]
JAL-1179 note and patch for exceptions raised when jalview.viewmodel.AlignmentViewport.getAlignmentView() called with non-null selection that contains no sequences. Needed for JAL-1031 and JAL-1032
jprocter [Tue, 25 Sep 2012 14:21:04 +0000 (15:21 +0100)]
JAL-1031 JAL-1032 if selection is non-null but empty, then calculate PCA or tree over whole view
jprocter [Tue, 25 Sep 2012 13:30:00 +0000 (14:30 +0100)]
JAL-1010 write validated value back to text field to ensure parameter value is always valid
jprocter [Tue, 25 Sep 2012 11:41:47 +0000 (12:41 +0100)]
JAL-970 JAL-1052 (comment about JAL-1140)
jprocter [Tue, 25 Sep 2012 11:38:02 +0000 (12:38 +0100)]
JAL-970 document interactive RNA secondary structure editing
jprocter [Tue, 25 Sep 2012 10:20:17 +0000 (11:20 +0100)]
JAL-1173 - trap redraw buffer OOM errors. needs a test case - since the dialog doesn't get raised reliably.
jprocter [Tue, 25 Sep 2012 10:19:15 +0000 (11:19 +0100)]
JAL-1173 try to catch OOMs when loading annotation onto alignment (need JAL-1176) to recover from these problems
jprocter [Tue, 25 Sep 2012 09:20:09 +0000 (10:20 +0100)]
JAL-1076 add note in documentation about Alt rather than Control enabling group editing in applet
jprocter [Mon, 24 Sep 2012 21:01:04 +0000 (22:01 +0100)]
JAL-1130 transparent big version for JNLP and file icon
jprocter [Mon, 24 Sep 2012 16:53:09 +0000 (17:53 +0100)]
JAL-958 revised applet parameter documentation to standardise on long form 'normaliseSequenceLogo', but still allow short form for legacy test pages.
jprocter [Mon, 24 Sep 2012 16:51:37 +0000 (17:51 +0100)]
formatting
jprocter [Mon, 24 Sep 2012 16:51:26 +0000 (17:51 +0100)]
JAL-958 normalise logo menu options in applet
jprocter [Mon, 24 Sep 2012 16:50:52 +0000 (17:50 +0100)]
JAL-958 enable logo display when normalise option selected
jprocter [Mon, 24 Sep 2012 16:49:15 +0000 (17:49 +0100)]
JAL-516 JAL-759 JAL-1066 group & group colourscheme always gets notified when group membership changes
jprocter [Mon, 24 Sep 2012 16:48:02 +0000 (17:48 +0100)]
only recalc group conservation after last sequence operated on in a bulk add/remove operation
jprocter [Mon, 24 Sep 2012 16:47:16 +0000 (17:47 +0100)]
JAL-516 JAL-759 JAL-1066 group & group colourscheme always gets notified when group membership changes
jprocter [Mon, 24 Sep 2012 16:39:34 +0000 (17:39 +0100)]
JAL-958 JAL-966 refactor group/alignment associated conservation, consensus and logo logic to core model
jprocter [Mon, 24 Sep 2012 08:10:36 +0000 (09:10 +0100)]
JAL-1130 remove lossy logo versions
jprocter [Fri, 21 Sep 2012 16:26:54 +0000 (17:26 +0100)]
Merge branch 'JAL-1130' into develop
git://source.jalview.org / jalview.git / log