gmungoc [Wed, 20 Feb 2019 12:15:06 +0000 (12:15 +0000)]
JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)
gmungoc [Tue, 19 Feb 2019 11:15:34 +0000 (11:15 +0000)]
JAL-3187 hacks to get peptide variant in to Jmol hover tooltip
gmungoc [Mon, 18 Feb 2019 09:19:14 +0000 (09:19 +0000)]
JAL-3187 reset ViewStyle on Cancel in FeatureSettings
gmungoc [Wed, 13 Feb 2019 14:36:54 +0000 (14:36 +0000)]
JAL-3187 'on top' optional for complementary features
Conflicts:
src/jalview/gui/FeatureSettings.java
gmungoc [Fri, 15 Feb 2019 07:43:15 +0000 (07:43 +0000)]
JAL-3010 getColumnClass() never return null
gmungoc [Fri, 25 Jan 2019 11:15:40 +0000 (11:15 +0000)]
JAL-3187 return a colour for linked features with transparency
gmungoc [Fri, 25 Jan 2019 10:54:38 +0000 (10:54 +0000)]
JAL-3187 set initial state of checkbox from viewport
gmungoc [Fri, 25 Jan 2019 09:19:31 +0000 (09:19 +0000)]
JAL-3187 don't compute variant features on peptide, show on demand
gmungoc [Wed, 23 Jan 2019 11:18:16 +0000 (11:18 +0000)]
JAL-3187 fix out by one feature on structure position
gmungoc [Wed, 23 Jan 2019 09:16:14 +0000 (09:16 +0000)]
Merge branch 'develop' into feature/JAL-3187linkedFeatures
gmungoc [Wed, 23 Jan 2019 09:15:52 +0000 (09:15 +0000)]
JAL-3063 correct handling of absent choice element in DBRef Mapping
gmungoc [Tue, 22 Jan 2019 14:39:47 +0000 (14:39 +0000)]
JAL-3187 clunky sort by renderorder in findComplementFeaturesAtResidue
gmungoc [Mon, 21 Jan 2019 15:58:32 +0000 (15:58 +0000)]
JAL-3187 also repaint complement on change in FeatureTypeSettings
gmungoc [Mon, 21 Jan 2019 15:32:06 +0000 (15:32 +0000)]
JAL-3187 draw complement features on alignment / structure
gmungoc [Mon, 21 Jan 2019 14:54:23 +0000 (14:54 +0000)]
JAL-3187 unit tests updated and errors caught
gmungoc [Mon, 21 Jan 2019 14:32:17 +0000 (14:32 +0000)]
JAL-3187 findFeaturesAtResidue answer in render order (tests TODO)
gmungoc [Mon, 21 Jan 2019 12:41:17 +0000 (12:41 +0000)]
JAL-3187 repaint a 'following' complementary view on change
gmungoc [Mon, 21 Jan 2019 11:47:49 +0000 (11:47 +0000)]
JAL-3187 (hacked up) show complement features on structure/Overview
gmungoc [Fri, 18 Jan 2019 15:12:46 +0000 (15:12 +0000)]
JAL-3187 basic first version for tooltips only (rendering yet to do)
Jim Procter [Thu, 17 Jan 2019 12:29:06 +0000 (12:29 +0000)]
JAL-3116 clear out whitespace when materialising Sequence object from Uniprot XML
Jim Procter [Wed, 16 Jan 2019 11:38:15 +0000 (11:38 +0000)]
Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop
Jim Procter [Tue, 15 Jan 2019 13:12:10 +0000 (13:12 +0000)]
JAL-1767 test that changing view association for PCA panel can be restored
Jim Procter [Tue, 15 Jan 2019 13:10:42 +0000 (13:10 +0000)]
JAL-1767 refactor associated view logic to public method and synchronise PCAPanel.av/ap with RotateableCanvac.ap/av
Jim Procter [Tue, 15 Jan 2019 11:19:39 +0000 (11:19 +0000)]
JAL-1767 patch buggy PCA view association test
gmungoc [Mon, 14 Jan 2019 16:13:10 +0000 (16:13 +0000)]
JAL-3186 remove Variable Colour from popup menu
gmungoc [Mon, 14 Jan 2019 16:00:59 +0000 (16:00 +0000)]
JAL-3186 remove duplicate message keys
gmungoc [Fri, 16 Nov 2018 08:04:54 +0000 (08:04 +0000)]
JAL-2069 wider dialog so all fields show!
Conflicts:
src/jalview/gui/FeatureTypeSettings.java
gmungoc [Mon, 14 Jan 2019 14:25:11 +0000 (14:25 +0000)]
JAL-2069 clear any error colour when setting threshold from slider
gmungoc [Wed, 26 Sep 2018 14:08:11 +0000 (15:08 +0100)]
JAL-3125 tidy up
gmungoc [Wed, 26 Sep 2018 11:05:01 +0000 (12:05 +0100)]
JAL-3125 avoid slider 'rounding' threshold field value
Jim Procter [Wed, 9 Jan 2019 17:29:21 +0000 (17:29 +0000)]
JAL-1767 failing test to check if the PCA view association is correctly saved and restored
Jim Procter [Wed, 9 Jan 2019 16:24:44 +0000 (16:24 +0000)]
Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767
Jim Procter [Wed, 9 Jan 2019 16:23:37 +0000 (16:23 +0000)]
JAL-3063 remove stale JAXB binding POJO
Jim Procter [Wed, 9 Jan 2019 16:22:03 +0000 (16:22 +0000)]
Merge branch 'feature/JAL-3063JAXB' into features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767
Jim Procter [Wed, 9 Jan 2019 16:16:45 +0000 (16:16 +0000)]
JAL-3063 - ant task for regenerating JAXB schema - could be optimised further
gmungoc [Thu, 3 Jan 2019 10:28:43 +0000 (10:28 +0000)]
JAL-1889 additional test for clover-added fields
gmungoc [Thu, 3 Jan 2019 09:16:15 +0000 (09:16 +0000)]
JAL-1889 ignore 'synthetic' fields added for jacoco
gmungoc [Fri, 21 Dec 2018 11:48:28 +0000 (11:48 +0000)]
JAL-1767 minimise local variable scope
Jim Procter [Thu, 20 Dec 2018 13:36:33 +0000 (13:36 +0000)]
JAL-1767 port save/load PCA panel to JAXB - JAL-3063
Jim Procter [Thu, 20 Dec 2018 11:46:25 +0000 (11:46 +0000)]
JAL-3171 JAL-3063 merge updates from JAL-1767
Jim Procter [Wed, 19 Dec 2018 16:53:33 +0000 (16:53 +0000)]
Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_across_views
gmungoc [Wed, 19 Dec 2018 11:38:30 +0000 (11:38 +0000)]
JAL-2791 JAL-2808 correct Javadoc for api method
gmungoc [Wed, 19 Dec 2018 09:16:41 +0000 (09:16 +0000)]
JAL-3032 ignore /site also on non-JS branches
Jim Procter [Tue, 18 Dec 2018 19:20:32 +0000 (19:20 +0000)]
JAL-2846 ahem - proper release note for this fix from KJVDH !
Jim Procter [Tue, 18 Dec 2018 19:13:05 +0000 (19:13 +0000)]
JAL-3178 known defect in release notes
Jim Procter [Mon, 17 Dec 2018 17:53:49 +0000 (17:53 +0000)]
JAL-3111 JAL-2846 release notes
Jim Procter [Mon, 17 Dec 2018 17:52:26 +0000 (17:52 +0000)]
Merge branch 'bug/JAL-2846' into develop
Jim Procter [Mon, 17 Dec 2018 17:39:40 +0000 (17:39 +0000)]
JAL-3111 tweaked release notes and documented JAL-2864
Jim Procter [Mon, 17 Dec 2018 17:30:44 +0000 (17:30 +0000)]
Merge branch 'bug/JAL-2864nullOverviewCanvas' into develop
Jim Procter [Mon, 17 Dec 2018 17:19:48 +0000 (17:19 +0000)]
JAL-2865 release notes
Jim Procter [Mon, 17 Dec 2018 17:04:56 +0000 (17:04 +0000)]
Merge branch 'bug/JAL-2750' into develop
Jim Procter [Mon, 17 Dec 2018 16:00:33 +0000 (16:00 +0000)]
Merge branch 'task/JAL-3174_fixed_filename_tests' into develop
Jim Procter [Mon, 17 Dec 2018 15:59:32 +0000 (15:59 +0000)]
JAL-3174 backout un-needed stacktrace for exception raised during testing (since we expect it)
Ben Soares [Mon, 17 Dec 2018 15:16:57 +0000 (15:16 +0000)]
JAL-3174 Merging in some test filename-case fixes
Jim Procter [Mon, 17 Dec 2018 14:31:06 +0000 (14:31 +0000)]
Merge branch 'bug/JAL-2541cutRelocateFeatures' into develop
Jim Procter [Mon, 17 Dec 2018 14:30:11 +0000 (14:30 +0000)]
JAL-2541 JAL-2822 release notes
Jim Procter [Mon, 17 Dec 2018 14:29:50 +0000 (14:29 +0000)]
JAL-3111 bump release 2.11 release to January 2019
Jim Procter [Mon, 17 Dec 2018 11:54:21 +0000 (11:54 +0000)]
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
Jim Procter [Fri, 14 Dec 2018 17:50:30 +0000 (17:50 +0000)]
JAL-3171 dataset reference tests now in Functional group
Jim Procter [Fri, 14 Dec 2018 17:44:25 +0000 (17:44 +0000)]
JAL-3171 record mapping between unmarshalled sequence’s dataset sequence ID and materialised dataset to allow belt-and-braces discovery of existing dataset - test now passes
Jim Procter [Fri, 14 Dec 2018 16:34:01 +0000 (16:34 +0000)]
JAL-3171 raise warning when a dataset reference exists *and* a different dataset exists for the sequenceSetID
Jim Procter [Fri, 14 Dec 2018 16:13:26 +0000 (16:13 +0000)]
JAL-3171 more complex project test - where sequences were copied from one alignment view into a new alignment and more views created.
Jim Procter [Fri, 14 Dec 2018 15:09:22 +0000 (15:09 +0000)]
JAL-3171 resolve dataset for imported projects via the alignment’s SequenceSetId
Jim Procter [Fri, 14 Dec 2018 12:28:24 +0000 (12:28 +0000)]
JAL-3171 failing test for legacy projects and fixing multiple dataset references
Jim Procter [Fri, 14 Dec 2018 11:59:45 +0000 (11:59 +0000)]
JAL-3171 register existing dataset for new view
Jim Procter [Fri, 14 Dec 2018 11:59:11 +0000 (11:59 +0000)]
JAL-3171 failing test checking preservation of dataset
gmungoc [Thu, 6 Dec 2018 10:06:25 +0000 (10:06 +0000)]
JAL-1854 fix Checkstyle import violations
gmungoc [Thu, 6 Dec 2018 10:05:57 +0000 (10:05 +0000)]
JAL-1854 Checkstyle updated to 8.12
gmungoc [Thu, 8 Nov 2018 15:34:57 +0000 (15:34 +0000)]
JAL-1889 ignore Clover instrumentation in test (second attempt)
gmungoc [Thu, 8 Nov 2018 15:24:06 +0000 (15:24 +0000)]
JAL-1889 unit test tweaks for running on server
gmungoc [Fri, 28 Sep 2018 11:29:55 +0000 (12:29 +0100)]
JAL-3063 service param files read/saved using JAXB not Castor binding
gmungoc [Fri, 28 Sep 2018 11:29:28 +0000 (12:29 +0100)]
JAL-3063 top level element added to JalviewWsParamSet.xsd
gmungoc [Fri, 28 Sep 2018 11:28:54 +0000 (12:28 +0100)]
JAL-3063 comments re use of xjc to generate Java binding classes
gmungoc [Mon, 24 Sep 2018 07:53:16 +0000 (08:53 +0100)]
JAL-3063 tidy commented out code
gmungoc [Fri, 21 Sep 2018 13:52:20 +0000 (14:52 +0100)]
JAL-3063 wrappers with check for null getting optional Integer, Float,
Boolean XML attributes
gmungoc [Thu, 20 Sep 2018 11:23:14 +0000 (12:23 +0100)]
JAL-2843 tweaks to help text for filters
gmungoc [Thu, 20 Sep 2018 10:54:31 +0000 (11:54 +0100)]
JAL-2843 help text for colour by attribute, feature filters
Jim Procter [Wed, 19 Sep 2018 14:45:29 +0000 (15:45 +0100)]
Merge branch 'bug/JAL-3120restoreFeatureColour' into develop
gmungoc [Wed, 19 Sep 2018 13:59:44 +0000 (14:59 +0100)]
JAL-3120 preserve plain colour value when changing to Colour by Label
gmungoc [Wed, 19 Sep 2018 12:44:58 +0000 (13:44 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Wed, 19 Sep 2018 11:39:17 +0000 (12:39 +0100)]
Merge branch 'cherrypick/JAL-2808_notabs' into develop
Jim Procter [Thu, 5 Jul 2018 13:38:42 +0000 (14:38 +0100)]
JAL-2808 JAL-3026 deleted all commented out tab code from the dialog
Omitted dialog refactoring from JAL-3058
gmungoc [Thu, 5 Jul 2018 13:27:44 +0000 (14:27 +0100)]
JAL-2808 JAL-3032 drop tabbed layout for Colours and Filters
gmungoc [Wed, 19 Sep 2018 08:07:49 +0000 (09:07 +0100)]
JAL-3063 use JAXB for 'Save as Project' and load project from parameter
gmungoc [Wed, 19 Sep 2018 07:03:38 +0000 (08:03 +0100)]
JAL-3063 unit test for save/load project switched to JAXB
gmungoc [Tue, 18 Sep 2018 16:43:03 +0000 (17:43 +0100)]
JAL-3063 Save/Load user defined colours using JAXB
gmungoc [Tue, 18 Sep 2018 15:58:25 +0000 (16:58 +0100)]
JAL-3063 Save/Load user colour scheme using JAXB
gmungoc [Tue, 18 Sep 2018 15:57:42 +0000 (16:57 +0100)]
JAL-3063 top level element added to colours schema, JAXB classes regen'd
gmungoc [Tue, 18 Sep 2018 15:18:13 +0000 (16:18 +0100)]
JAL-3063 New View via JAXB
gmungoc [Tue, 18 Sep 2018 15:03:09 +0000 (16:03 +0100)]
JAL-3063 temporary extra menu option to save/load project as JAXB
gmungoc [Tue, 18 Sep 2018 15:02:34 +0000 (16:02 +0100)]
JAL-3063 first version of Jalview2XML using JAXB to (un)marshal
gmungoc [Tue, 18 Sep 2018 15:01:52 +0000 (16:01 +0100)]
JAL-3063 JAXB binding classes generated by xjc from jalview.xsd
gmungoc [Tue, 18 Sep 2018 15:01:07 +0000 (16:01 +0100)]
JAL-3063 tweak schema so JAXB tool xjc recognises XML root element
gmungoc [Tue, 18 Sep 2018 15:00:20 +0000 (16:00 +0100)]
JAL-3063 tweak schema so JAXB generates enums for enumerated values
Jim Procter [Tue, 18 Sep 2018 14:01:56 +0000 (15:01 +0100)]
JAL-2865 release notes
gmungoc [Mon, 17 Sep 2018 10:51:43 +0000 (11:51 +0100)]
JAL-3116 test method renamed to match code
gmungoc [Mon, 17 Sep 2018 10:47:51 +0000 (11:47 +0100)]
JAL-3116 unit tests adapted to EMBL over JAXB
gmungoc [Fri, 14 Sep 2018 16:11:40 +0000 (17:11 +0100)]
JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)
gmungoc [Thu, 13 Sep 2018 15:28:27 +0000 (16:28 +0100)]
JAL-3116 Uniprot XML unmarshalled using JAXB not Castor
gmungoc [Wed, 12 Sep 2018 15:30:52 +0000 (16:30 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
git://source.jalview.org / jalview.git / log