kiramt [Wed, 7 Jun 2017 08:14:37 +0000 (09:14 +0100)]
JAL-2591 Overview window update interrupts
kiramt [Mon, 5 Jun 2017 06:51:49 +0000 (07:51 +0100)]
JAL-2571 Missed (alwaysRun=true) for @BeforeMethod
Jim Procter [Sun, 4 Jun 2017 15:12:13 +0000 (16:12 +0100)]
JAL-2228 java 1.7 compliance
Jim Procter [Sun, 4 Jun 2017 12:27:45 +0000 (13:27 +0100)]
JAL-2291 updated docs
Jim Procter [Sun, 4 Jun 2017 12:18:38 +0000 (13:18 +0100)]
JAL-2291 only hide/show columns intersecting with currently selected region.
Jim Procter [Sun, 4 Jun 2017 12:18:27 +0000 (13:18 +0100)]
JAL-2291 get bitset representing hidden columns
Jim Procter [Sun, 4 Jun 2017 11:17:31 +0000 (12:17 +0100)]
JAL-2291 use HiddenColumns.hideMarkedBits and take union of selection and sequence under popup
Jim Procter [Sun, 4 Jun 2017 11:05:49 +0000 (12:05 +0100)]
JAL-2291 method taking a BitSet for hiding columns
Jim Procter [Sun, 4 Jun 2017 11:04:31 +0000 (12:04 +0100)]
JAL-2291 bug fix - BitSet.set is [start,end+1)
Jim Procter [Sun, 4 Jun 2017 11:02:16 +0000 (12:02 +0100)]
JAL-2291 fixed broken asserts for SequenceI.getInsertionsAsBits
Jim Procter [Sun, 4 Jun 2017 09:43:01 +0000 (10:43 +0100)]
JAL-2291 ‘Hide Insertions’ now operates on selection or if none available, the sequence that was right-clicked on.
Jim Procter [Sun, 4 Jun 2017 09:41:56 +0000 (10:41 +0100)]
JAL-2291 SequenceI.getInsertionsAsBits for convenient logical operations
Jim Procter [Sun, 4 Jun 2017 09:03:39 +0000 (10:03 +0100)]
JAL-2582 comment about IDs being lost if they resembl ensembl IDs but can’t be resolved to a genomic ID.
Jim Procter [Sun, 4 Jun 2017 09:01:54 +0000 (10:01 +0100)]
JAL-2582 recognise ENS…P peptide IDs and make two getParent requests to get gene ID.
Jim Procter [Fri, 2 Jun 2017 16:11:15 +0000 (17:11 +0100)]
Merge branch 'bug/JAL-2578' into develop
Jim Procter [Fri, 2 Jun 2017 16:04:38 +0000 (17:04 +0100)]
Merge branch 'bug/JAL-2577' into develop
Jim Procter [Fri, 2 Jun 2017 15:58:12 +0000 (16:58 +0100)]
Merge branch 'features/JAL-2228_featureSetCounts_minRangeTweak' into develop
tcofoegbu [Fri, 2 Jun 2017 14:29:25 +0000 (15:29 +0100)]
JAL-2473 revised default minimum dimension for Alignment Frame windows
Jim Procter [Fri, 2 Jun 2017 13:12:21 +0000 (14:12 +0100)]
JAL-2228 always create zero score annotations, since select/hide annotation filter ignores null positions in rows
Jim Procter [Fri, 2 Jun 2017 13:11:30 +0000 (14:11 +0100)]
JAL-2228 always set minimum for count to zero for annotation row
kiramt [Fri, 2 Jun 2017 13:00:13 +0000 (14:00 +0100)]
JAL-2577 Don't allow viewport ranges below 0. Unit tests updated.
kiramt [Fri, 2 Jun 2017 08:59:22 +0000 (09:59 +0100)]
JAL-2578 Moved hidden columns reveal to before selection adjustment
Jim Procter [Thu, 1 Jun 2017 13:17:05 +0000 (14:17 +0100)]
Merge branch 'features/JAL-1648_cache_user_inputs' into develop
Jim Procter [Wed, 31 May 2017 21:02:55 +0000 (22:02 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 21:02:41 +0000 (22:02 +0100)]
JAL-2418 release notes for JAL-2547, JAL-2563, JAL-1256
Jim Procter [Wed, 31 May 2017 20:23:52 +0000 (21:23 +0100)]
Merge branch 'JAL-2571' into develop
Jim Procter [Wed, 31 May 2017 20:21:59 +0000 (21:21 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 31 May 2017 20:10:33 +0000 (21:10 +0100)]
JAL-2398 - updated groovy script for direct field modification
Jim Procter [Wed, 31 May 2017 20:07:04 +0000 (21:07 +0100)]
JAL-2418 JAL-2563 release notes
Jim Procter [Wed, 31 May 2017 20:06:31 +0000 (21:06 +0100)]
JAL-2418 typo
Jim Procter [Wed, 31 May 2017 20:05:39 +0000 (21:05 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
tcofoegbu [Wed, 31 May 2017 10:46:22 +0000 (11:46 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 31 May 2017 10:46:08 +0000 (11:46 +0100)]
JAL-2375 fix unit test to reflect improvement
tcofoegbu [Wed, 31 May 2017 10:08:24 +0000 (11:08 +0100)]
Fixed failing tests
tcofoegbu [Wed, 31 May 2017 09:59:45 +0000 (10:59 +0100)]
JAL-2533 updated unit test to reflect improvement
gmungoc [Wed, 31 May 2017 08:00:46 +0000 (09:00 +0100)]
JAL-2547 handle contact features 'around' a gap correctly
kiramt [Tue, 30 May 2017 18:28:42 +0000 (19:28 +0100)]
JAL-2573 Fixes for alignment < viewport width, and similarly height
gmungoc [Tue, 30 May 2017 15:01:44 +0000 (16:01 +0100)]
JAL-2547 tooltip/AmendFeatures on gap straddled by feature, not for
adjacent feature
kiramt [Tue, 30 May 2017 09:36:34 +0000 (10:36 +0100)]
JAL-2571 Corrected alignment width/height checks to visible only
gmungoc [Tue, 30 May 2017 09:26:46 +0000 (10:26 +0100)]
JAL-2570 don't zap group colour scheme when mapping over split frame
Jim Procter [Mon, 29 May 2017 16:38:34 +0000 (17:38 +0100)]
Merge branch 'bug/JAL-2034contextchange' into develop
Jim Procter [Mon, 29 May 2017 16:35:35 +0000 (17:35 +0100)]
JAL-2388 release notes
tcofoegbu [Mon, 29 May 2017 14:12:17 +0000 (15:12 +0100)]
JAL-1648 improvement on finder searchbox keyboard control - Enter to update search box if popup is displayed otherwise perform find next action
Jim Procter [Mon, 29 May 2017 14:00:18 +0000 (15:00 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:58:33 +0000 (14:58 +0100)]
JAL-2520 properly documented as a fixed bug in release notes
Jim Procter [Mon, 29 May 2017 13:26:21 +0000 (14:26 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 13:25:40 +0000 (14:25 +0100)]
JAL-2465,JAL-2520,JAL-2533 release notes
Jim Procter [Mon, 29 May 2017 13:19:41 +0000 (14:19 +0100)]
Merge branch 'features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url' into develop
Jim Procter [Mon, 29 May 2017 13:07:47 +0000 (14:07 +0100)]
JAL-2533 update javadoc
Jim Procter [Mon, 29 May 2017 12:51:59 +0000 (13:51 +0100)]
JAL-2465 fixed groups for JmolViewerTest.testStructureLoadingViaURL
tcofoegbu [Mon, 29 May 2017 12:05:05 +0000 (13:05 +0100)]
JAL-1648 code fix - enter key should pick selected item on finder searchbox
Jim Procter [Mon, 29 May 2017 11:18:53 +0000 (12:18 +0100)]
Merge branch 'bug/JAL-2536' into develop
Jim Procter [Mon, 29 May 2017 11:18:09 +0000 (12:18 +0100)]
JAL-2536 tweak javadoc wording
Jim Procter [Mon, 29 May 2017 11:10:54 +0000 (12:10 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Mon, 29 May 2017 11:10:33 +0000 (12:10 +0100)]
JAL-2517 release notes
Jim Procter [Mon, 29 May 2017 10:52:46 +0000 (11:52 +0100)]
Merge branch 'bug/JAL-2517cancelAppletColour' into develop
Jim Procter [Mon, 29 May 2017 10:50:01 +0000 (11:50 +0100)]
release notes
JAL-2550 known defect
JAL-2535 stockholm->PP annotation
Jim Procter [Mon, 29 May 2017 10:01:19 +0000 (11:01 +0100)]
JAL-2418 updated JABAWS server in what’s new
Jim Procter [Mon, 29 May 2017 10:00:56 +0000 (11:00 +0100)]
JAL-2491 JAL-2526 JAL-2566 JAL-2563 JAL-2547 release notes
Jim Procter [Sat, 27 May 2017 13:16:18 +0000 (14:16 +0100)]
Merge branch 'bug/JAL-2491' into develop
Jim Procter [Sat, 27 May 2017 13:02:54 +0000 (14:02 +0100)]
Merge branch 'bug/JAL-2547tooltipOnGap' into develop
Jim Procter [Sat, 27 May 2017 13:01:59 +0000 (14:01 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 13:01:41 +0000 (14:01 +0100)]
JAL-2563 failing test to verify SetStatus returns position and message includes the position for ambiguous peptide ‘B’.
Jim Procter [Sat, 27 May 2017 13:00:49 +0000 (14:00 +0100)]
JAL-2563 test to verify SetStatus returns -1 so mouseOver events are raised via StructureSelectionManager (JAL-2491, expected fixed by JAL-2547)
Jim Procter [Sat, 27 May 2017 11:58:30 +0000 (12:58 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 11:57:37 +0000 (12:57 +0100)]
JAL-2547 JAL-2562 rejig SetStatusMessage return value test for legibility and maximum assert coverage before JAL-2526 causes failure
Jim Procter [Sat, 27 May 2017 11:41:43 +0000 (12:41 +0100)]
Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
Jim Procter [Sat, 27 May 2017 11:32:09 +0000 (12:32 +0100)]
JAL-2526 test and documentation for SeqPanel.setStatus behaviour needed to fix bug noted on JAL-2491 where mouseover at gap highlights position for sequence to right of gap in complementary view.
Jim Procter [Sat, 27 May 2017 10:25:02 +0000 (11:25 +0100)]
JAL-2562 javadoc TODO
kiramt [Fri, 26 May 2017 21:11:00 +0000 (22:11 +0100)]
JAL-2491 Missed port to applet from JAL-1691
Jim Procter [Fri, 26 May 2017 16:37:57 +0000 (17:37 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Fri, 26 May 2017 16:37:31 +0000 (17:37 +0100)]
JAL-2418 updated JPred documentation and screenshot for JPred4
Jim Procter [Fri, 26 May 2017 16:37:07 +0000 (17:37 +0100)]
JAL-2418 JAL-2549 JABAWS 2.2 release notes
Jim Procter [Fri, 26 May 2017 15:29:20 +0000 (16:29 +0100)]
Merge branch 'features/JAL-2549_updateJABAWSto220' into develop
tcofoegbu [Fri, 26 May 2017 14:27:16 +0000 (15:27 +0100)]
JAL-2465 Improvement to re-instate storing recently opened URLs for alignments loaded from a structure format via URL
tcofoegbu [Fri, 26 May 2017 13:48:44 +0000 (14:48 +0100)]
JAL-2465 fix to prevent files loaded from the system's temporary directory from being included in recently opend files store
tcofoegbu [Fri, 26 May 2017 11:46:34 +0000 (12:46 +0100)]
Merge branch 'features/JAL-1648_cache_user_inputs' of https://source.jalview.org/git/jalview into features/JAL-1648_cache_user_inputs
tcofoegbu [Fri, 26 May 2017 11:35:43 +0000 (12:35 +0100)]
JAL-1648 fix to transfer focus back to alignment frame when Finder window is close via hitting cancel or the excape key
Jim Procter [Thu, 25 May 2017 16:16:27 +0000 (17:16 +0100)]
Merge branch 'develop' into features/JAL-1648_cache_user_inputs
bugfixes in finder for feature creation and minimum window size merged to topic
kiramt [Thu, 25 May 2017 13:31:51 +0000 (14:31 +0100)]
JAl-2034 Ported to applet
kiramt [Thu, 25 May 2017 13:06:38 +0000 (14:06 +0100)]
JAL-2034 don't update overview after click without drag on group
kiramt [Thu, 25 May 2017 07:49:08 +0000 (08:49 +0100)]
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange
kiramt [Wed, 24 May 2017 12:47:58 +0000 (13:47 +0100)]
JAL-2551 Fix to group colouring when group extent is reduced
kiramt [Wed, 24 May 2017 09:44:47 +0000 (10:44 +0100)]
JAL-2034 Added isDefined flag to SequenceGroup
Jim Procter [Tue, 23 May 2017 19:39:17 +0000 (20:39 +0100)]
JAL-2549 RNAAliFold result to annotation file roundtrip test fails test due to JAL-2550 - Upper/lower case alphabet recognised as WUSS RNA annotation
Jim Procter [Tue, 23 May 2017 19:35:59 +0000 (20:35 +0100)]
JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get supported services list
Jim Procter [Tue, 23 May 2017 19:35:23 +0000 (20:35 +0100)]
JAL-2549 replace JABAWS 2.1 with 2.2 client and remove JPredWS client and tests
gmungoc [Tue, 23 May 2017 11:55:08 +0000 (12:55 +0100)]
JAL-2547 don't show features in tooltip over a gap
gmungoc [Mon, 22 May 2017 14:37:32 +0000 (15:37 +0100)]
JAL-2504 update the right feature colour when creating a new feature
gmungoc [Mon, 22 May 2017 13:39:57 +0000 (14:39 +0100)]
JAL-2544 unit tests for sort by feature score
gmungoc [Mon, 22 May 2017 13:33:07 +0000 (14:33 +0100)]
JAL-2544 check feature overlaps selection region
kiramt [Mon, 22 May 2017 10:57:47 +0000 (11:57 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-2256' into develop
Jim Procter [Mon, 22 May 2017 10:34:46 +0000 (11:34 +0100)]
JAL-2418 patch build - broken htsjdk import
gmungoc [Fri, 19 May 2017 15:59:48 +0000 (16:59 +0100)]
JAL-2526 removed redundant call to Sequence.findPosition()
Jim Procter [Thu, 18 May 2017 15:33:00 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-2388_typeCheckAlignView.getUpdatedView' into develop
Jim Procter [Thu, 18 May 2017 15:31:27 +0000 (16:31 +0100)]
JAL-2388 return empty hidden columns for fully visible alignment view
kiramt [Thu, 18 May 2017 13:09:21 +0000 (14:09 +0100)]
JAL-2256 Corrected AllCols/Rows iterator behaviour for single element
Jim Procter [Thu, 18 May 2017 11:18:14 +0000 (12:18 +0100)]
JAL-2418 remove explicit test suite stats
Jim Procter [Wed, 17 May 2017 15:26:52 +0000 (16:26 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 17 May 2017 15:10:15 +0000 (16:10 +0100)]
Merge branch 'bug/JAL-2510amendFeatures' into develop
git://source.jalview.org / jalview.git / log