Jim Procter [Thu, 11 Jul 2013 12:58:09 +0000 (13:58 +0100)]
Merge branch 'JAL-1347' into develop
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 09:51:11 +0000 (10:51 +0100)]
Merge branch 'JAL-895/reopen' into develop
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 12:49:09 +0000 (13:49 +0100)]
Merge branch 'Release_2_8_1_Branch' into develop
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 12:19:49 +0000 (13:19 +0100)]
Merge branch 'structures/JAL-1016' into develop
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 18:06:14 +0000 (19:06 +0100)]
Merge branch 'bug/JAL-1230' into develop
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 12:59:57 +0000 (13:59 +0100)]
Merge branch 'bug/JAL-1230' into develop
Jim Procter [Sun, 23 Jun 2013 12:58:51 +0000 (13:58 +0100)]
Merge commit '72c628b' into develop
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 13:17:42 +0000 (14:17 +0100)]
Merge branch 'feature/JAL-1330' into develop
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 13:12:56 +0000 (14:12 +0100)]
Merge branch 'JAL-1294_iupredexportimport' into develop
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 10:36:50 +0000 (11:36 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into develop
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 16:01:05 +0000 (17:01 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into develop
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 [Tue, 18 Jun 2013 16:06:38 +0000 (17:06 +0100)]
JAL-674 - avoid java.util.ConcurrentModificationException on the pdbfile list
Jim Procter [Tue, 18 Jun 2013 16:03:08 +0000 (17:03 +0100)]
JAL-674 tests for PDB ID retrieval and specific chain retrieval
Jim Procter [Mon, 17 Jun 2013 17:26:54 +0000 (18:26 +0100)]
Merge branch 'JAL-1319_jronn_npe' into develop
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
Jim Procter [Mon, 17 Jun 2013 16:52:15 +0000 (17:52 +0100)]
Merge branch 'JAL-1312_ambiguity_na' into develop
Jim Procter [Mon, 17 Jun 2013 16:51:33 +0000 (17:51 +0100)]
Merge branch 'JAL-1312_ambiguity_na' into Release_2_8_Branch
Jim Procter [Mon, 17 Jun 2013 16:45:23 +0000 (17:45 +0100)]
JAL-1027 fix errors in alternative codon table
Jim Procter [Mon, 17 Jun 2013 16:45:03 +0000 (17:45 +0100)]
JAL-1027 check that ResidueProperties.codonHash2 is actually identical to the codon table used in previous versions
Jim Procter [Mon, 17 Jun 2013 16:41:40 +0000 (17:41 +0100)]
JAL-1027 use alternative codon table in ResidueProperties.codonHash2 for translation
Jim Procter [Mon, 17 Jun 2013 14:23:00 +0000 (15:23 +0100)]
JAL-1035 option to allow 'STOP' codon to translate as '*'
Jim Procter [Mon, 17 Jun 2013 14:14:40 +0000 (15:14 +0100)]
JAL-1312 patch for regression noticed after patch to jalview.analysis.Dna cdna translation
Jim Procter [Mon, 17 Jun 2013 14:13:13 +0000 (15:13 +0100)]
JAL-1312 rewrite of code for first reported exception - note - maintaining scontigs may not even be necessary !
Jim Procter [Mon, 17 Jun 2013 14:10:22 +0000 (15:10 +0100)]
JAL-1312 formatting and more comprehensive test
Jim Procter [Mon, 17 Jun 2013 14:09:04 +0000 (15:09 +0100)]
JAL-1312 remove unnecessary methods
Jim Procter [Mon, 17 Jun 2013 12:52:21 +0000 (13:52 +0100)]
JAL-1312 more helpful error message when translation breaks
Jim Procter [Mon, 17 Jun 2013 09:40:26 +0000 (10:40 +0100)]
JAL-529 - IUBMB nucleotide ambiguity codes and programmatic generation of codons and inverse tables
Jim Procter [Mon, 17 Jun 2013 09:35:28 +0000 (10:35 +0100)]
JAL-1318 - route warnings to stderr (need to find a better solution for JAL-1069)
Jim Procter [Mon, 17 Jun 2013 09:33:11 +0000 (10:33 +0100)]
JAL-1318 avoid failure if SequenceI objects don't have valid dataset references
Jim Procter [Mon, 17 Jun 2013 09:31:58 +0000 (10:31 +0100)]
JAL-966 avoid using java.util.Vector
Jim Procter [Mon, 17 Jun 2013 09:21:32 +0000 (10:21 +0100)]
test for JAL-1312
Jim Procter [Fri, 14 Jun 2013 15:23:31 +0000 (16:23 +0100)]
Merge branch 'JAL-1316' into develop
Jim Procter [Fri, 14 Jun 2013 15:23:22 +0000 (16:23 +0100)]
Merge branch 'JAL-1316' into Release_2_8_Branch
Jim Procter [Fri, 14 Jun 2013 15:18:23 +0000 (16:18 +0100)]
JAL-1316 compact '' to '
Jim Procter [Fri, 14 Jun 2013 15:17:58 +0000 (16:17 +0100)]
JAL-1316 recognise and extract quoted region as nodename
Jim Procter [Fri, 14 Jun 2013 14:06:42 +0000 (15:06 +0100)]
JAL-1316 JAL-1313 newick IO test harness
Jim Procter [Thu, 13 Jun 2013 16:38:24 +0000 (17:38 +0100)]
Merge branch 'JAL-1314_headlessFlag' into develop
Jim Procter [Thu, 13 Jun 2013 16:38:08 +0000 (17:38 +0100)]
Merge branch 'JAL-1314_headlessFlag' into Release_2_8_Branch
Jim Procter [Thu, 13 Jun 2013 16:37:43 +0000 (17:37 +0100)]
JAL-1314 allow 'nogui' and 'headless' as synonyms for 'nodisplay' argument and ensure awt.gui.headless=true is set as early as possible.
Jim Procter [Thu, 13 Jun 2013 16:36:46 +0000 (17:36 +0100)]
JAL-1314 test for common variants of -nodisplay performing the same for EPS generation
JAL-1314 test for identical termination behaviour with/without java.awt.headless=true
Jim Procter [Thu, 13 Jun 2013 15:55:18 +0000 (16:55 +0100)]
Merge branch 'JAL-1315_headlessEPS' into develop
Jim Procter [Thu, 13 Jun 2013 15:55:11 +0000 (16:55 +0100)]
Merge branch 'JAL-1315_headlessEPS' into Release_2_8_Branch
Jim Procter [Thu, 13 Jun 2013 15:53:33 +0000 (16:53 +0100)]
fix for JAL-1315
Jim Procter [Thu, 13 Jun 2013 15:53:10 +0000 (16:53 +0100)]
JAL-1315 test for exit and successful generation of EPS using commandline
Jim Procter [Tue, 11 Jun 2013 10:50:27 +0000 (11:50 +0100)]
change to release version of VARNA-3-9
Jim Procter [Sun, 9 Jun 2013 18:34:47 +0000 (19:34 +0100)]
JAL-674 avoid runtime dependency on annotate3d webservice in applet
Jim Procter [Sun, 9 Jun 2013 18:33:54 +0000 (19:33 +0100)]
JAL-674 - update applet build dependency on VARNA
Jim Procter [Sun, 9 Jun 2013 14:30:55 +0000 (15:30 +0100)]
Merge branch '2_8_1_patch_multiharmony' into develop
Jim Procter [Sun, 9 Jun 2013 14:30:33 +0000 (15:30 +0100)]
Merge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch
Jim Procter [Sun, 9 Jun 2013 14:29:43 +0000 (15:29 +0100)]
fix for JAL-1298
Jim Procter [Sun, 9 Jun 2013 14:29:14 +0000 (15:29 +0100)]
JAL-715 - TODO
Jim Procter [Fri, 7 Jun 2013 15:33:07 +0000 (16:33 +0100)]
Merge branch '2_8_1_patch_multiharmony' into develop
Jim Procter [Fri, 7 Jun 2013 15:32:54 +0000 (16:32 +0100)]
Merge branch '2_8_1_patch_multiharmony' into Release_2_8_Branch
Jim Procter [Fri, 7 Jun 2013 12:31:37 +0000 (13:31 +0100)]
JAL-1309 fix broken partition computation for adding in ungrouped sequences as final group
Jim Procter [Fri, 7 Jun 2013 12:24:47 +0000 (13:24 +0100)]
JAL-945 uniquify prior to submission
Jim Procter [Fri, 7 Jun 2013 12:24:16 +0000 (13:24 +0100)]
formatting
Jim Procter [Fri, 7 Jun 2013 12:24:08 +0000 (13:24 +0100)]
JAL-715 allow headless construction for testing
Jim Procter [Fri, 7 Jun 2013 12:23:28 +0000 (13:23 +0100)]
JAL-724 JAL-715 refactor and create new test for RSBS framework and Multi-harmony service
Jim Procter [Tue, 4 Jun 2013 13:23:08 +0000 (14:23 +0100)]
fix for JAL-1246
git://source.jalview.org / jalview.git / log