Jim Procter [Tue, 29 Apr 2014 12:25:46 +0000 (13:25 +0100)]
Merge branch 'JAL-1340_redundancy' into develop
Jim Procter [Mon, 28 Apr 2014 12:32:52 +0000 (13:32 +0100)]
JAL-1340 mark redundant sequences as soon as redundancy calculation has finished
Jim Procter [Mon, 28 Apr 2014 12:31:59 +0000 (13:31 +0100)]
JAL-1340 simpler and more efficient interactive highlighting of redundant sequences
Jim Procter [Mon, 28 Apr 2014 12:28:17 +0000 (13:28 +0100)]
JAL-1340 ensure slider value wide enough to see three figures
Jim Procter [Sun, 27 Apr 2014 22:15:33 +0000 (23:15 +0100)]
Merge branch 'JAL-1322' into develop
Jim Procter [Sun, 27 Apr 2014 22:15:11 +0000 (23:15 +0100)]
Merge branch 'JAL-1322' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 22:14:24 +0000 (23:14 +0100)]
JAL-1322 avoid rounding error causing non functional slider and allow slider to reach maximum value for parameter
Jim Procter [Sun, 27 Apr 2014 22:13:58 +0000 (23:13 +0100)]
JAL-1322 allow slider to reach maximum value for parameter
Jim Procter [Sun, 27 Apr 2014 22:12:56 +0000 (23:12 +0100)]
JAL-1322 only update slider when return is pressed
Jim Procter [Sun, 27 Apr 2014 20:41:36 +0000 (21:41 +0100)]
Merge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 20:41:29 +0000 (21:41 +0100)]
Merge branch 'JAL-1164_regression' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 20:41:06 +0000 (21:41 +0100)]
Merge branch 'JAL-952_rnahelix' into develop
Conflicts:
src/jalview/schemes/ColourSchemeProperty.java
Jim Procter [Sun, 27 Apr 2014 20:36:44 +0000 (21:36 +0100)]
Merge branch 'JAL-1164_regression' into develop
Jim Procter [Sun, 27 Apr 2014 17:44:12 +0000 (18:44 +0100)]
workaround for JAL-1319 - catch unexpected NPE thrown by JABA client method
Jim Procter [Sun, 27 Apr 2014 17:38:13 +0000 (18:38 +0100)]
JAL-1164 (regression) reinstate 'apply disorder prediction to selection' functionality in 2.8.1+ lost during JabaCalcWorker refactoring
Jim Procter [Sun, 27 Apr 2014 15:59:31 +0000 (16:59 +0100)]
JAL-952 JAL-1268 document TCoffee and RNA helices colourschemes in applet properties
Jim Procter [Sun, 27 Apr 2014 15:22:18 +0000 (16:22 +0100)]
JAL-952 JAL-1268 document RNA Helices and T-Coffee Scores as valid colour scheme names for applet parameters
Jim Procter [Sun, 27 Apr 2014 15:17:11 +0000 (16:17 +0100)]
JAL-952 JAL-1268 add RNA Helices and T-Coffee to list of available colour schemes in jalview preferences
Jim Procter [Sun, 27 Apr 2014 15:16:41 +0000 (16:16 +0100)]
JAL-952 resolve colour scheme as 'RNA Helices'
Jim Procter [Sun, 27 Apr 2014 15:12:42 +0000 (16:12 +0100)]
JAL-952 refactor code to select annotation for colouring the alignment
Jim Procter [Sun, 27 Apr 2014 15:06:09 +0000 (16:06 +0100)]
test for JAL-952
Jim Procter [Fri, 25 Apr 2014 16:15:36 +0000 (17:15 +0100)]
Merge branch 'JAL-1177_prop_rnasecstr' into develop
Conflicts:
src/jalview/schemes/ColourSchemeProperty.java
-- whitespace conflicts only
Jim Procter [Fri, 25 Apr 2014 16:11:28 +0000 (17:11 +0100)]
Merge branch 'JAL-1177_prop_rnasecstr' into Release_2_8_1_Branch
Jim Procter [Fri, 25 Apr 2014 16:10:10 +0000 (17:10 +0100)]
fix for JAL-1268
Jim Procter [Fri, 25 Apr 2014 16:09:55 +0000 (17:09 +0100)]
test for JAL-1268
Jim Procter [Fri, 25 Apr 2014 13:27:23 +0000 (14:27 +0100)]
JAL-1177 additional saveState calls to write a dataset only jalview xml document
Jim Procter [Fri, 25 Apr 2014 13:26:04 +0000 (14:26 +0100)]
JAL-1177 patches to loader to cope with dataset only jalview xml documents
Jim Procter [Fri, 25 Apr 2014 13:24:56 +0000 (14:24 +0100)]
JAL-1177 new flag to write a dataset only jalview XML document
Jim Procter [Fri, 25 Apr 2014 13:20:42 +0000 (14:20 +0100)]
JAL-1177 allow jalview alignments to be saved that have no alignment views, to support storage of parent datasets
Jim Procter [Fri, 25 Apr 2014 12:51:34 +0000 (13:51 +0100)]
JAL-1177 propagate sequence associated annotation to dataset sequence
Jim Procter [Fri, 25 Apr 2014 12:50:47 +0000 (13:50 +0100)]
JAL-1177 refactored command line test harness
Jim Procter [Fri, 25 Apr 2014 12:49:44 +0000 (13:49 +0100)]
test for JAL-1177 store and recover RNA secondary structure for a stockholm file with sequence associated RNA structure
Jim Procter [Thu, 24 Apr 2014 16:39:58 +0000 (17:39 +0100)]
JAL-1232 fix - ensure display all columns flag is set if an RNA helix is created on an annotation row.
Jim Procter [Wed, 23 Apr 2014 16:16:21 +0000 (17:16 +0100)]
Merge branch 'JAL-1486_hiddenStartEnd' into develop
Jim Procter [Wed, 23 Apr 2014 16:15:57 +0000 (17:15 +0100)]
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch
Jim Procter [Wed, 23 Apr 2014 16:15:04 +0000 (17:15 +0100)]
JAL-1486 todo for 2.8.2 release
Jim Procter [Wed, 23 Apr 2014 15:37:53 +0000 (16:37 +0100)]
Merge branch 'jims_marckhacks' into develop
Jim Procter [Wed, 23 Apr 2014 15:37:13 +0000 (16:37 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 21:25:17 +0000 (22:25 +0100)]
JAL-1458 updated logo for installer
Jim Procter [Mon, 21 Apr 2014 20:21:36 +0000 (21:21 +0100)]
JAL-1383 scrubbed envision GUI and documentation
Jim Procter [Mon, 21 Apr 2014 17:39:55 +0000 (18:39 +0100)]
JAL-1355 keys for colours
Jim Procter [Mon, 21 Apr 2014 17:13:56 +0000 (18:13 +0100)]
fix for JAL-1438
Jim Procter [Mon, 21 Apr 2014 16:42:05 +0000 (17:42 +0100)]
Merge branch 'jims_marckhacks' into develop
Jim Procter [Mon, 21 Apr 2014 16:32:38 +0000 (17:32 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 16:27:19 +0000 (17:27 +0100)]
JAL-1473 define defaults for DNA/Protein PCA calculation
Jim Procter [Mon, 21 Apr 2014 16:26:52 +0000 (17:26 +0100)]
JAL-1485 JAL-1483 show i18n key for different available score models, and limit to those applicable for a protein / DNA
Jim Procter [Mon, 21 Apr 2014 16:24:56 +0000 (17:24 +0100)]
JAL-1473 JAL-1355 i18n for score model submenu
Jim Procter [Mon, 21 Apr 2014 16:23:57 +0000 (17:23 +0100)]
JAL-1485 JAL-1473 use compound i18n messages to construct title of tree using translations of score model and calculation method
Jim Procter [Mon, 21 Apr 2014 16:21:23 +0000 (17:21 +0100)]
JAL-1485
Jim Procter [Mon, 21 Apr 2014 15:06:30 +0000 (16:06 +0100)]
JAL-1484 always update the dataset sequence if 'trimDatasetSeqs' option is not set.
Jim Procter [Mon, 21 Apr 2014 15:02:03 +0000 (16:02 +0100)]
JAL-1466 don't include empty columns if no upstream sequence data available for aligned subsequences
Jim Procter [Mon, 21 Apr 2014 15:00:45 +0000 (16:00 +0100)]
JAL-1355 JAL-1466 i18n for flanking sequence menu entry and tooltip messages
Jim Procter [Mon, 21 Apr 2014 13:24:56 +0000 (14:24 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Sat, 19 Apr 2014 12:56:18 +0000 (13:56 +0100)]
JAL-741 (poss related JAL-971) - fix NPE raised when attempting to sort alignment by feature when lots of groups displayed
Jim Procter [Sat, 19 Apr 2014 12:53:11 +0000 (13:53 +0100)]
JAL-1476 JAL-1016 avoid NPE messiness if structures fail to align for some reason
Jim Procter [Sat, 19 Apr 2014 12:46:03 +0000 (13:46 +0100)]
don't unhook existing group associated annotation JAL-1480
Jim Procter [Fri, 18 Apr 2014 15:22:38 +0000 (16:22 +0100)]
fix for JAL-1478
Jim Procter [Fri, 18 Apr 2014 15:18:36 +0000 (16:18 +0100)]
JAL-1478 test to demonstrate bug
Jim Procter [Fri, 18 Apr 2014 14:17:42 +0000 (15:17 +0100)]
JAL-1477 tooltip
Jim Procter [Fri, 18 Apr 2014 09:56:53 +0000 (10:56 +0100)]
JAL-1476 - don't send broken commands to Jmol when no columns exist to superimpose structures
Jim Procter [Fri, 18 Apr 2014 09:50:15 +0000 (10:50 +0100)]
JAL-1477 first implementation of 'View all representative structures' option.
Jim Procter [Fri, 18 Apr 2014 09:14:54 +0000 (10:14 +0100)]
JAL-1466 import full length sequence to dataset sequence or trim it to local sequence's length
Jim Procter [Fri, 18 Apr 2014 09:12:40 +0000 (10:12 +0100)]
JAL-1466 flag and jalview_properties setting to control retrieval of full length dataset sequence
Jim Procter [Fri, 18 Apr 2014 09:08:57 +0000 (10:08 +0100)]
JAL-1466 improved test and patched off by one that deleted one dataset residue from flanking alignment
Jim Procter [Tue, 15 Apr 2014 17:50:12 +0000 (18:50 +0100)]
JAL-1466 new calculation menu option to recover the full width sequences either side of the current alignment and append them.
Jim Procter [Tue, 15 Apr 2014 17:47:56 +0000 (18:47 +0100)]
tidy imports
Jim Procter [Tue, 15 Apr 2014 17:43:34 +0000 (18:43 +0100)]
patch v2 for JAL-1474 add the newly recovered dataset sequence to the dataset currently being build/operated on if it isn't already present
Jim Procter [Tue, 15 Apr 2014 17:42:48 +0000 (18:42 +0100)]
patch v1 for JAL-1474 - make sure we actually set the dataset sequence's string
Jim Procter [Tue, 15 Apr 2014 17:41:57 +0000 (18:41 +0100)]
JAL-1474 note about buggy 'merge sequence' operation pointing to relevant issue
Jim Procter [Tue, 15 Apr 2014 17:11:07 +0000 (18:11 +0100)]
JAL-1473 tree calcs performed with ScoreModelI instances
Jim Procter [Tue, 15 Apr 2014 15:23:35 +0000 (16:23 +0100)]
don't finness the alignment annotation modification methods by modifying the vector directly!
Jim Procter [Tue, 15 Apr 2014 15:21:02 +0000 (16:21 +0100)]
patch for JAL-1465 - set min/max thresholds for each disorder annotation row
Jim Procter [Tue, 15 Apr 2014 15:19:50 +0000 (16:19 +0100)]
JAL-1473 menu entries for different score models available for NJ/UPGMA tree building (note - this will not scale well!)
Jim Procter [Tue, 15 Apr 2014 15:16:26 +0000 (16:16 +0100)]
JAL-1473 provide Amino acid physicochemical conservation based score matrices
Jim Procter [Tue, 15 Apr 2014 15:15:36 +0000 (16:15 +0100)]
JAL-1473 show available score matrices for use in PCA calculation
Jim Procter [Tue, 15 Apr 2014 15:09:20 +0000 (16:09 +0100)]
JAL-1473 refactor score matrices and tree score calculations to interface/api and base implementations
Jim Procter [Tue, 15 Apr 2014 14:40:35 +0000 (15:40 +0100)]
JAL-1355 missing message
Jim Procter [Sun, 6 Apr 2014 11:29:11 +0000 (12:29 +0100)]
fix for JAL-1464 avoid NPE with per-sequence annotation with no positional elements as generated by 'extract scores' (related to JAL-1066)
Jim Procter [Sat, 5 Apr 2014 12:24:15 +0000 (13:24 +0100)]
Merge branch 'r281_JAL-1211' into develop
Jim Procter [Sat, 5 Apr 2014 12:23:27 +0000 (13:23 +0100)]
Merge branch 'r281_JAL-1211' into Release_2_8_1_Branch
Jim Procter [Fri, 4 Apr 2014 15:38:24 +0000 (16:38 +0100)]
JAL-1211 - set annotation panel height according to the amount of annotation present on the alignment and the relative size of the alignment.
Jim Procter [Fri, 4 Apr 2014 15:18:24 +0000 (16:18 +0100)]
JAL-1211 - pick up site-defined defined window geometry before we calculate layout
Jim Procter [Fri, 4 Apr 2014 15:16:58 +0000 (16:16 +0100)]
fix for JAL-1461 - check that filetype setting in browser is non-null
Jim Procter [Fri, 4 Apr 2014 13:36:57 +0000 (14:36 +0100)]
Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_Branch
Jim Procter [Fri, 4 Apr 2014 13:35:53 +0000 (14:35 +0100)]
JAL-1335 typo and 'edit' action
jprocter [Thu, 20 Mar 2014 16:03:37 +0000 (16:03 +0000)]
Merge branch 'JAL-1459_dnd' into develop
jprocter [Thu, 20 Mar 2014 15:53:03 +0000 (15:53 +0000)]
JAL-1459 ensure we notify the drop handler that we've dealt with the
drop event
Jim Procter [Wed, 26 Feb 2014 17:23:11 +0000 (17:23 +0000)]
Merge branch 'JAL-1226' into develop
Jim Procter [Wed, 26 Feb 2014 17:23:03 +0000 (17:23 +0000)]
Merge branch 'JAL-1226' into Release_2_8_1_Branch_i18n
Jim Procter [Wed, 26 Feb 2014 17:22:58 +0000 (17:22 +0000)]
Merge branch 'JAL-1226' into Release_2_8_1_Branch
Jim Procter [Wed, 26 Feb 2014 17:22:38 +0000 (17:22 +0000)]
fix for JAL-1226
Jim Procter [Wed, 26 Feb 2014 16:21:03 +0000 (16:21 +0000)]
Merge branch 'JAL-686' into Release_2_8_1_Branch_i18n
Jim Procter [Wed, 26 Feb 2014 16:20:53 +0000 (16:20 +0000)]
Merge branch 'JAL-686' into develop
Jim Procter [Wed, 26 Feb 2014 16:20:43 +0000 (16:20 +0000)]
Merge branch 'JAL-686' into Release_2_8_1_Branch
Jim Procter [Wed, 26 Feb 2014 16:19:34 +0000 (16:19 +0000)]
JAL-1457 refactoring to explore why '-' appear in annotation rows (see AlignmentAnnotation.padGaps)
Jim Procter [Wed, 26 Feb 2014 16:14:31 +0000 (16:14 +0000)]
fix for JAL-686 - don't trim spaces before creating annotation
Jim Procter [Tue, 25 Feb 2014 16:50:29 +0000 (16:50 +0000)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Jim Procter [Tue, 25 Feb 2014 16:49:49 +0000 (16:49 +0000)]
Merge branch 'JAL-1454_patch' into develop
Jim Procter [Tue, 25 Feb 2014 16:49:39 +0000 (16:49 +0000)]
Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch
Jim Procter [Tue, 25 Feb 2014 16:48:58 +0000 (16:48 +0000)]
JAL-1355 typo in key
git://source.jalview.org / jalview.git / log