kiramt [Tue, 30 May 2017 18:28:42 +0000 (19:28 +0100)]
JAL-2573 Fixes for alignment < viewport width, and similarly height
kiramt [Tue, 30 May 2017 09:36:34 +0000 (10:36 +0100)]
JAL-2571 Corrected alignment width/height checks to visible only
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 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
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
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
Jim Procter [Wed, 17 May 2017 14:50:14 +0000 (15:50 +0100)]
JAL-2447 add links to issues.jalview.org for experimental features
Jim Procter [Wed, 17 May 2017 14:41:04 +0000 (15:41 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Wed, 17 May 2017 14:39:43 +0000 (15:39 +0100)]
JAL-2447 experimental section in ‘Whats New’
Jim Procter [Wed, 17 May 2017 14:39:17 +0000 (15:39 +0100)]
JAL-2447 JAL-2295 JAL-2296 documenting as experimental features
Jim Procter [Wed, 17 May 2017 13:46:38 +0000 (14:46 +0100)]
Merge branch 'develop' into documentation/JAL-2418_release2102
Jim Procter [Wed, 17 May 2017 13:31:54 +0000 (14:31 +0100)]
Merge branch 'features/JAL-2447experimentalFlag' into develop
Jim Procter [Wed, 17 May 2017 13:28:08 +0000 (14:28 +0100)]
JAL-2418 release notes
gmungoc [Wed, 17 May 2017 12:07:13 +0000 (13:07 +0100)]
JAL-2504 use (and update) defaults for new feature only if not supplied
gmungoc [Wed, 17 May 2017 07:59:07 +0000 (08:59 +0100)]
Merge branch 'develop' into bug/JAL-2510amendFeatures
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
Jim Procter [Tue, 16 May 2017 16:36:01 +0000 (17:36 +0100)]
Merge branch 'documentation/JAL-2418_release2102' into develop
Jim Procter [Tue, 16 May 2017 16:27:35 +0000 (17:27 +0100)]
JAL-2418 release notes
Jim Procter [Tue, 16 May 2017 15:51:31 +0000 (16:51 +0100)]
JAL-384 documentation on custom colours groovy examples
Jim Procter [Tue, 16 May 2017 15:35:15 +0000 (16:35 +0100)]
JAL-384 - groovy scripts for conserved/unconserved colourscheme requests
Jim Procter [Tue, 16 May 2017 15:30:07 +0000 (16:30 +0100)]
JAL-2418 release notes
kiramt [Tue, 16 May 2017 15:10:07 +0000 (16:10 +0100)]
JAL-2536 Overview window sizing not subject to min size restrictions
Jim Procter [Tue, 16 May 2017 13:54:17 +0000 (14:54 +0100)]
JAL-2418 JAL-2316 added to new features
Jim Procter [Tue, 16 May 2017 13:30:04 +0000 (14:30 +0100)]
JAL-2316 tweaking docs and links in help
gmungoc [Tue, 16 May 2017 13:10:40 +0000 (14:10 +0100)]
JAL-2517 restore complex colour scheme on Cancel in User Defined Colours
Jim Procter [Tue, 16 May 2017 12:46:14 +0000 (13:46 +0100)]
JAL-2418 release 2.10.2 release notes template
Jim Procter [Tue, 16 May 2017 12:45:29 +0000 (13:45 +0100)]
alternative patch for JAL-2339 readability in java-help
gmungoc [Tue, 16 May 2017 12:40:27 +0000 (13:40 +0100)]
JAL-2403 simplify instantiation / configuration of score model for view
kiramt [Tue, 16 May 2017 10:34:09 +0000 (11:34 +0100)]
JAL-2522 Missed fix to applet
kiramt [Tue, 16 May 2017 09:37:48 +0000 (10:37 +0100)]
JAL-2388 Rationalised hashCode method in HiddenColumns
kiramt [Tue, 16 May 2017 09:15:40 +0000 (10:15 +0100)]
Merge branch 'develop' into bug/JAL-2491
kiramt [Tue, 16 May 2017 09:10:03 +0000 (10:10 +0100)]
JAL-2491 Better merge
Jim Procter [Tue, 16 May 2017 08:48:31 +0000 (09:48 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
Jim Procter [Mon, 15 May 2017 18:23:56 +0000 (19:23 +0100)]
JAL-2507 fix test: knockon from capitalisation on secondary structure from stockholm file
Jim Procter [Mon, 15 May 2017 16:37:43 +0000 (17:37 +0100)]
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop
Jim Procter [Mon, 15 May 2017 16:37:17 +0000 (17:37 +0100)]
JAL-2311 disable and relocate Jared service tests to Network (prior to their removal)
Jim Procter [Mon, 15 May 2017 16:26:53 +0000 (17:26 +0100)]
JAL-2507 capitalisation for annotation lines generated from stockholm annotation
Jim Procter [Mon, 15 May 2017 15:56:06 +0000 (16:56 +0100)]
JAL-2507 case insensitive recognition of annotation type
gmungoc [Mon, 15 May 2017 15:55:54 +0000 (16:55 +0100)]
JAL-2532 new feature types and colour changes from Amend Features
retained after Cancel in Feature Settings
Jim Procter [Mon, 15 May 2017 15:43:12 +0000 (16:43 +0100)]
JAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testAlignmentEquivalent asserts
Jim Procter [Mon, 15 May 2017 15:26:02 +0000 (16:26 +0100)]
JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0..9, ‘*’ or any other non-whitespace symbol parsed as ’10’.
tcofoegbu [Mon, 15 May 2017 15:07:09 +0000 (16:07 +0100)]
JAL-2520 improvement to use URL leaf name for creating temp file for URL file download
tcofoegbu [Mon, 15 May 2017 14:52:56 +0000 (15:52 +0100)]
JAL-2533 improvement to prune off file extension when imported seqs are named with the data file
kiramt [Mon, 15 May 2017 14:50:28 +0000 (15:50 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Mon, 15 May 2017 14:50:07 +0000 (15:50 +0100)]
JAL-2388 Add missed optimisation
kiramt [Mon, 15 May 2017 11:27:53 +0000 (12:27 +0100)]
JAL-2491 Better merge but not quite right yet
Jim Procter [Mon, 15 May 2017 11:14:20 +0000 (12:14 +0100)]
Merge branch 'features/JAL-2376_add-horizontal-bar' into develop
Jim Procter [Mon, 15 May 2017 11:07:39 +0000 (12:07 +0100)]
JAL-2371 create a default ResidueShader when constructing the viewport
kiramt [Mon, 15 May 2017 10:42:01 +0000 (11:42 +0100)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2491
(not working yet)
Conflicts:
src/jalview/appletgui/AlignmentPanel.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/OverviewPanel.java
src/jalview/gui/SeqPanel.java
src/jalview/viewmodel/OverviewDimensions.java
src/jalview/viewmodel/ViewportRanges.java
test/jalview/viewmodel/OverviewDimensionsTest.java
kiramt [Mon, 15 May 2017 08:42:17 +0000 (09:42 +0100)]
JAL-2491 Tests
kiramt [Mon, 15 May 2017 08:23:59 +0000 (09:23 +0100)]
JAL-2491 Tidies
git://source.jalview.org / jalview.git / log