Jim Procter [Mon, 7 Oct 2013 16:39:06 +0000 (17:39 +0100)]
JAL-1385 refactor logic to AlignmentViewController
Jim Procter [Mon, 7 Oct 2013 16:33:16 +0000 (17:33 +0100)]
JAL-1385 JAL-535 refactor sequence colour settings to abstract alignment view model
Jim Procter [Mon, 7 Oct 2013 16:02:45 +0000 (17:02 +0100)]
JAL-1385 expose core view model methods in interface
Jim Procter [Mon, 7 Oct 2013 15:59:52 +0000 (16:59 +0100)]
JAL-1385 Alignment view controller logic implementation and API
Jim Procter [Sat, 5 Oct 2013 14:02:04 +0000 (15:02 +0100)]
Merge branch 'JAL-1378_jb2.1cli' into Release_2_8_1_Branch
Jim Procter [Sat, 5 Oct 2013 13:01:00 +0000 (14:01 +0100)]
JAL-1379 graceful degradation to legacy service when JABAWS Jpred service not available
Jim Procter [Sat, 5 Oct 2013 12:59:40 +0000 (13:59 +0100)]
JAL-1379 JAL-1378 exclusion list property to ignore services not fully integrated with Jalview
Jim Procter [Sat, 5 Oct 2013 11:20:52 +0000 (12:20 +0100)]
JAL-1378 hack to place 'Predictors' into Secondary struture predictors (may be redacted later)
Jim Procter [Sat, 5 Oct 2013 11:20:15 +0000 (12:20 +0100)]
JAL-1364 use gapMap to map RNAalifold annotation onto correct columns
Jim Procter [Sat, 5 Oct 2013 11:13:12 +0000 (12:13 +0100)]
JAL-1379 JAL-1358 only enable/disable menu entries associated with services not applicable for the current sequence type
Jim Procter [Fri, 4 Oct 2013 15:27:01 +0000 (16:27 +0100)]
JAL-1383 - disable startup of the Envision2 workflow discovery thread
Jim Procter [Fri, 4 Oct 2013 15:22:16 +0000 (16:22 +0100)]
JAL-940 JAL-1378 EOL comment on JWS v1 services
Jim Procter [Fri, 4 Oct 2013 14:08:38 +0000 (15:08 +0100)]
update JABA client dependency in InstallAnywhere build
Jim Procter [Fri, 4 Oct 2013 14:07:00 +0000 (15:07 +0100)]
Merge branch 'RNAalifold' into Release_2_8_1_Branch
Jim Procter [Fri, 4 Oct 2013 14:03:52 +0000 (15:03 +0100)]
fix for JAL-1380 and efficiency todo for JAL-1381
Jim Procter [Fri, 4 Oct 2013 12:48:34 +0000 (13:48 +0100)]
JAL-1378 JWS-71 update to from-source build of JABA v2.1 client for use with JABA test server
Jim Procter [Wed, 25 Sep 2013 15:36:24 +0000 (16:36 +0100)]
JAL-1365 test that RNAAliFold service settings are stored and recovered from Jalview projects
Jim Procter [Wed, 25 Sep 2013 15:34:55 +0000 (16:34 +0100)]
formatting
Jim Procter [Wed, 25 Sep 2013 15:33:41 +0000 (16:33 +0100)]
JAL-1365 unified GUI building for AACon and RNAAliFold service clients
Jim Procter [Wed, 25 Sep 2013 15:30:37 +0000 (16:30 +0100)]
JAL-1365 use AlignAnalysisUIText class to provide metadata for a service's UI elements
Jim Procter [Wed, 25 Sep 2013 15:28:31 +0000 (16:28 +0100)]
JAL-1365 refactored core methods from RNAAliFold and AACon service clients to a common Alignment Analysis client class
Jim Procter [Wed, 25 Sep 2013 15:17:07 +0000 (16:17 +0100)]
JAL-1365 new metadata class to describe instantaneous calculation services like AACon and RNAAliFold
Jim Procter [Wed, 25 Sep 2013 15:13:56 +0000 (16:13 +0100)]
JAL-1270 nominal jalview version string for projects written during development tests
Jim Procter [Wed, 25 Sep 2013 15:10:43 +0000 (16:10 +0100)]
JAL-1270 Desktop.instance is null during headless jalview tests
Jim Procter [Fri, 20 Sep 2013 17:33:14 +0000 (18:33 +0100)]
formatting
Jim Procter [Tue, 3 Sep 2013 13:27:54 +0000 (14:27 +0100)]
Merge branch 'JAL-1373_precision' into RNAalifold
Jim Procter [Tue, 3 Sep 2013 13:27:29 +0000 (14:27 +0100)]
Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch
Jim Procter [Tue, 3 Sep 2013 13:26:47 +0000 (14:26 +0100)]
JAL-1373 tweak precision calculation so alignments of less than 100 sequences don't include any decimal points.
Jim Procter [Tue, 3 Sep 2013 13:25:28 +0000 (14:25 +0100)]
JAL-920 compute a consensus for single sequence
Jim Procter [Mon, 2 Sep 2013 17:14:07 +0000 (18:14 +0100)]
Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch
Jim Procter [Mon, 2 Sep 2013 17:11:29 +0000 (18:11 +0100)]
JAL-1373 JAL-520 wrap tooltips for columns in annotation rows
Jim Procter [Mon, 2 Sep 2013 17:09:08 +0000 (18:09 +0100)]
JAL-1373 generate percentages with appropriate precision
Jim Procter [Mon, 2 Sep 2013 17:07:42 +0000 (18:07 +0100)]
JAL-1373 pass size of sequence set to consensus rendering routines so appropriate precision can be chosen
Jim Procter [Mon, 2 Sep 2013 09:42:43 +0000 (10:42 +0100)]
JAL-1358 monday morning commits :(
Jim Procter [Mon, 2 Sep 2013 09:37:45 +0000 (10:37 +0100)]
JAL-1358 jabaws not jaba
Jim Procter [Mon, 2 Sep 2013 09:27:46 +0000 (10:27 +0100)]
JAL-1358 update jabaws client for installanywhere
Jim Procter [Mon, 2 Sep 2013 09:20:21 +0000 (10:20 +0100)]
JAL-1358 remove old v2 jaba min-client
Daniel Barton [Sat, 31 Aug 2013 16:42:19 +0000 (17:42 +0100)]
Brief html documentation entry for RNAalifold under webServices
Daniel Barton [Fri, 30 Aug 2013 16:11:12 +0000 (17:11 +0100)]
Colour be RNA helices bug fixed
Daniel Barton [Fri, 30 Aug 2013 12:18:55 +0000 (13:18 +0100)]
JAL-1358 Cleaned up RNAalifoldClient.java. RNA helices colouring bug and parameters bug unsolved
Daniel Barton [Wed, 28 Aug 2013 21:23:50 +0000 (22:23 +0100)]
RNAalifoldClient updated to be more like AAConClient and now (attempts) to support all the output from RNAalifold
Daniel Barton [Tue, 27 Aug 2013 16:37:06 +0000 (17:37 +0100)]
JAL-1358 jalview displays some RNA struture annotation but the format is very messed up
Jim Procter [Tue, 27 Aug 2013 15:08:37 +0000 (16:08 +0100)]
Merge branch 'JAL-1359_patch' into Release_2_8_1_Branch
Jim Procter [Tue, 27 Aug 2013 15:08:17 +0000 (16:08 +0100)]
JAL-1359 simpler logic for deciding if all threads have finished.
Note: I couldn't reproduce the JAL-1359 bug after rebuilding my JABAWS development server - so trust me on this fix :)
Daniel Barton [Tue, 27 Aug 2013 15:04:37 +0000 (16:04 +0100)]
Merge remote-tracking branch 'origin/Release_2_8_1_Branch' into RNAalifold
Daniel Barton [Tue, 27 Aug 2013 15:04:26 +0000 (16:04 +0100)]
JAL-1358 RNAStructExportImport test file mirrors DisorderAnnotExportImport file. RNAalifoldClient updated to basic working state.
Jim Procter [Tue, 27 Aug 2013 14:46:19 +0000 (15:46 +0100)]
Merge branch 'JAL-1332_regression' into Release_2_8_1_Branch
Jim Procter [Tue, 27 Aug 2013 14:42:06 +0000 (15:42 +0100)]
JAL-1332 regression from
7ce72ca7fadf35a249427ecb836b22abb04ab653 - allow 'null' context to be used (for test/src/jalview/ws/jabaws/TestDisorderAnnotExportImport where Desktop is not created before an AlignFrame is constructed)
Jim Procter [Tue, 27 Aug 2013 14:40:50 +0000 (15:40 +0100)]
JAL-1332 - defer SSM provision to root provider for the alignment view
Daniel Barton [Tue, 27 Aug 2013 12:47:23 +0000 (13:47 +0100)]
JAL-1358 Just the eclipse project/classpath files so that I can stash changes and demonstrate DisorderAnnotExportImport failure
Daniel Barton [Thu, 22 Aug 2013 13:06:52 +0000 (14:06 +0100)]
Jalview builds sucessfully and runs from eclipse
Jim Procter [Tue, 20 Aug 2013 16:28:34 +0000 (17:28 +0100)]
Merge branch 'JAL-1353-bugdemo' into Release_2_8_1_Branch
Jim Procter [Tue, 20 Aug 2013 16:27:16 +0000 (17:27 +0100)]
JAL-1353 test demonstrating the freeze with minimal jalview code dependency
Jim Procter [Fri, 12 Jul 2013 15:58:53 +0000 (16:58 +0100)]
Merge branch 'JAL-1347' into Release_2_8_1_Branch
Jim Procter [Fri, 12 Jul 2013 15:58:22 +0000 (16:58 +0100)]
JAL-1347 RNA Structure consensus follows the alignment viewport consensus rendering settings in version 2.8.x
Jim Procter [Fri, 12 Jul 2013 15:57:45 +0000 (16:57 +0100)]
JAL-1347 flow control for display of profile data is upstream from this method
Jim Procter [Thu, 11 Jul 2013 12:57:54 +0000 (13:57 +0100)]
Merge branch 'JAL-1347' into Release_2_8_1_Branch
Jim Procter [Thu, 11 Jul 2013 12:57:03 +0000 (13:57 +0100)]
JAL-1347 identify and set rendering settings for consensus annotation rows
JAL-966 Note - should abstract this logic even further away in Jalview v3
Jim Procter [Thu, 11 Jul 2013 12:54:25 +0000 (13:54 +0100)]
JAL-1347 refactor logic for setting display flags for histogram and profile to main control loop
Jim Procter [Thu, 11 Jul 2013 12:53:27 +0000 (13:53 +0100)]
JAL-1347 make it efficient to call getConsensus to test identity of alignment annotation rows
Jim Procter [Tue, 9 Jul 2013 09:50:55 +0000 (10:50 +0100)]
Merge branch 'JAL-895/reopen' into Release_2_8_1_Branch
Jim Procter [Tue, 9 Jul 2013 09:49:10 +0000 (10:49 +0100)]
JAL-895 - patch example files with correct Fe positions
Jim Procter [Mon, 8 Jul 2013 12:48:56 +0000 (13:48 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_Branch
Jim Procter [Mon, 8 Jul 2013 12:48:09 +0000 (13:48 +0100)]
make sure 'example alignment' can be found in documentation
Jim Procter [Sun, 7 Jul 2013 12:19:41 +0000 (13:19 +0100)]
Merge branch 'structures/JAL-1016' into Release_2_8_Branch
Jim Procter [Sun, 7 Jul 2013 12:08:52 +0000 (13:08 +0100)]
JAL-1345 - set nSeconds arg for chemapps.stolaf.edu/jmol/docs/#compare according to total number of superpositions
Jim Procter [Sun, 7 Jul 2013 11:44:25 +0000 (12:44 +0100)]
JAL-1016 Instruct user to report situations where the race condition still happens
Jim Procter [Sun, 7 Jul 2013 11:42:59 +0000 (12:42 +0100)]
JAL-1332 make SSM context discovery safer (particularly in plugin context)
Jim Procter [Sun, 7 Jul 2013 11:39:43 +0000 (12:39 +0100)]
JAL-583 refactor todo about separating code to construct Jmol superposition from the code that obtains the atom matching used to construct the expression
Jim Procter [Sun, 7 Jul 2013 11:39:23 +0000 (12:39 +0100)]
fix for JAL-1016 - wait around until we have a complete set of PDB filename mappings available in Jmol
Jim Procter [Sun, 7 Jul 2013 11:38:02 +0000 (12:38 +0100)]
JAL-1016 - do our assertions immediatly
Jim Procter [Sun, 23 Jun 2013 18:06:23 +0000 (19:06 +0100)]
Merge branch 'bug/JAL-1230' into Release_2_8_Branch
Jim Procter [Sun, 23 Jun 2013 18:05:42 +0000 (19:05 +0100)]
JAL-1230 update alignment state for annotation edits, and validate annotation panel height to ensure any autocalculated annotation is made visible
Jim Procter [Sun, 23 Jun 2013 18:03:53 +0000 (19:03 +0100)]
JAL-1230 proxy method for synchronising internal AlignmentI state in response to changes in alignment annotation
Jim Procter [Sun, 23 Jun 2013 18:02:20 +0000 (19:02 +0100)]
JAL-1230 simplify initialisation of consensus, conservation and structure consensus rows
Jim Procter [Sun, 23 Jun 2013 13:00:05 +0000 (14:00 +0100)]
Merge branch 'bug/JAL-1230' into Release_2_8_Branch
Jim Procter [Sun, 23 Jun 2013 12:58:40 +0000 (13:58 +0100)]
Merge commit '72c628b' into Release_2_8_Branch
Jim Procter [Sat, 22 Jun 2013 13:17:34 +0000 (14:17 +0100)]
Merge branch 'feature/JAL-1330' into Release_2_8_Branch
Jim Procter [Sat, 22 Jun 2013 13:17:14 +0000 (14:17 +0100)]
JAL-1330 pick primary seqeunce data source for authority rather than first node of sub tree
Jim Procter [Fri, 21 Jun 2013 16:20:03 +0000 (17:20 +0100)]
JAL-1230 comment unused code to avoid NPE
Jim Procter [Fri, 21 Jun 2013 14:09:01 +0000 (15:09 +0100)]
JAL-1327 TODO
Jim Procter [Fri, 21 Jun 2013 14:08:37 +0000 (15:08 +0100)]
JAL-1326 JAL-1327 update all graphline thresholds with flag for interactive or final adjustment event
Jim Procter [Fri, 21 Jun 2013 13:29:41 +0000 (14:29 +0100)]
JAL-1241 - generate colour for all annotation values within range
Jim Procter [Fri, 21 Jun 2013 13:12:49 +0000 (14:12 +0100)]
Merge branch 'JAL-1294_iupredexportimport' into Release_2_8_Branch
Jim Procter [Fri, 21 Jun 2013 12:59:53 +0000 (13:59 +0100)]
JAL-1325 formatting
Jim Procter [Fri, 21 Jun 2013 12:59:35 +0000 (13:59 +0100)]
JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF for GRAPHLINE statements
Jim Procter [Fri, 21 Jun 2013 12:58:42 +0000 (13:58 +0100)]
JAL-1294 JAL-1325 store graphline for individual annotation rows.
Jim Procter [Fri, 21 Jun 2013 11:20:11 +0000 (12:20 +0100)]
JAL-1294 JAL-1325 bugfix equals
Jim Procter [Fri, 21 Jun 2013 10:58:47 +0000 (11:58 +0100)]
JAL-1294 JAL-1325 test annotation threshold line equivalence
Jim Procter [Fri, 21 Jun 2013 10:36:17 +0000 (11:36 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
Jim Procter [Fri, 21 Jun 2013 10:35:07 +0000 (11:35 +0100)]
JAL-1127 set option widgets to service defaults only when showing default settings
Jim Procter [Wed, 19 Jun 2013 16:41:27 +0000 (17:41 +0100)]
JAL-1240 avoid NPE when source has no proxy available
Jim Procter [Wed, 19 Jun 2013 16:00:37 +0000 (17:00 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
Jim Procter [Tue, 18 Jun 2013 20:57:45 +0000 (21:57 +0100)]
JAL-1320 ascending alphabetical order
Jim Procter [Tue, 18 Jun 2013 20:57:02 +0000 (21:57 +0100)]
JAL-1320 preserve option/parameter order with LinkedHashMap
Jim Procter [Tue, 18 Jun 2013 20:38:16 +0000 (21:38 +0100)]
JAL-1320 sort options and parameters according to their name
Jim Procter [Tue, 18 Jun 2013 20:29:29 +0000 (21:29 +0100)]
typo
Jim Procter [Tue, 18 Jun 2013 20:28:57 +0000 (21:28 +0100)]
JAL-1321 don't show a tooltip for empty strings
Jim Procter [Mon, 17 Jun 2013 17:26:47 +0000 (18:26 +0100)]
Merge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch
Jim Procter [Mon, 17 Jun 2013 17:25:54 +0000 (18:25 +0100)]
JAL-1319 (blacklist fix) check for presence of a score object before we start making annotation
git://source.jalview.org / jalview.git / log