Jim Procter [Fri, 18 Jan 2019 14:18:57 +0000 (14:18 +0000)]
Merge branch 'feature/JAL-3063jaxbNoCastor' into feature/JAL-3141_Create_a_backup_when_saving_projects_and_other_files
JAL-3063 switched from castor to JAXB - backupFile bits added to jalview.project.Jalview2XML
Jim Procter [Fri, 18 Jan 2019 14:06:09 +0000 (14:06 +0000)]
Merge branch 'develop' into feature/JAL-3063jaxbNoCastor
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
Ben Soares [Wed, 16 Jan 2019 14:27:12 +0000 (14:27 +0000)]
JAL-3141 Remove no longer used exampleLabel
Jim Procter [Wed, 16 Jan 2019 11:50:22 +0000 (11:50 +0000)]
Merge branch 'feature/JAL-3063jaxbNoCastor' into develop
JAL-3063 todo: add castor-1.1-cycle.jar back to libraries inorder to ensure VAMSAS functionality remains
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
Ben Soares [Mon, 14 Jan 2019 23:53:16 +0000 (23:53 +0000)]
JAL-3141 Forgot this file, sorry!
Ben Soares [Mon, 14 Jan 2019 23:47:38 +0000 (23:47 +0000)]
JAL-3141 Added a 'Save Project as...' File menu item, always asks for filename. Altered 'Save Project' File menu item to automatically save if both 1) projectFile is set (e.g. loaded or previously saved), 2) Backups is enabled
Ben Soares [Mon, 14 Jan 2019 23:40:48 +0000 (23:40 +0000)]
JAL-3141 Made more constants
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
Ben Soares [Wed, 9 Jan 2019 18:29:05 +0000 (18:29 +0000)]
JAL-3141 removed redundant method to tests
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 16:24:20 +0000 (16:24 +0000)]
Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
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 16:19:57 +0000 (16:19 +0000)]
Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
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
Ben Soares [Wed, 9 Jan 2019 08:45:11 +0000 (08:45 +0000)]
JAL-3141 language word ending corrections
Ben Soares [Wed, 9 Jan 2019 08:26:07 +0000 (08:26 +0000)]
JAL-3141 Added i18n for the example filenames in Preferences
Ben Soares [Wed, 9 Jan 2019 07:58:32 +0000 (07:58 +0000)]
JAL-3141 forgot to add this file after extracting the class!
Ben Soares [Wed, 9 Jan 2019 00:26:07 +0000 (00:26 +0000)]
JAL-3141 Made one more suggested change from code review
Ben Soares [Tue, 8 Jan 2019 23:22:10 +0000 (23:22 +0000)]
JAL-3141 Made some more suggested changes from code review
Ben Soares [Tue, 8 Jan 2019 23:13:08 +0000 (23:13 +0000)]
JAL-3141 Made some suggested changes from code review
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 [Mon, 3 Dec 2018 15:03:53 +0000 (15:03 +0000)]
JAL-3063 Castor removed from codebase
gmungoc [Mon, 3 Dec 2018 14:19:18 +0000 (14:19 +0000)]
Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
Ben Soares [Tue, 20 Nov 2018 11:43:13 +0000 (11:43 +0000)]
.gitignore changes
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
Ben Soares [Mon, 5 Nov 2018 10:01:18 +0000 (10:01 +0000)]
JAL-3141 Slightly improved message and more thorough tests
Ben Soares [Mon, 5 Nov 2018 08:57:38 +0000 (08:57 +0000)]
JAL-3141 couple of minor fixes for example files being displayed in the Preferences tab
Ben Soares [Fri, 2 Nov 2018 16:37:33 +0000 (16:37 +0000)]
JAL-3141 Tests now available and working, bringing to light a problem with the classInit flag (now removed). Added some more dodgy Spanish translations.
Ben Soares [Thu, 1 Nov 2018 14:27:00 +0000 (14:27 +0000)]
JAL-3141 Preferences 'Backups' tab now fits. Moved initial option setting into Preferences with all the other preference initial setting.
Ben Soares [Wed, 31 Oct 2018 17:04:19 +0000 (17:04 +0000)]
JAL-3141 Preferences 'Backups' tab now working. Doesn't fit in default space though -- needs adjusting
Ben Soares [Thu, 25 Oct 2018 15:36:41 +0000 (16:36 +0100)]
JAL-3141 Ostensibly all backups working for alignment and project saves. Need to add a preferences tab and some tests.
Ben Soares [Wed, 24 Oct 2018 12:23:27 +0000 (13:23 +0100)]
JAL-3141 Code checkout. Not compiling.
Ben Soares [Wed, 24 Oct 2018 12:22:50 +0000 (13:22 +0100)]
JAL-3141 Code checkout. Not compiling.
Ben Soares [Tue, 23 Oct 2018 17:03:52 +0000 (18:03 +0100)]
BackupFilter and other unfinished business
Ben Soares [Mon, 22 Oct 2018 16:10:38 +0000 (17:10 +0100)]
JAL-3141 Taken the backing up code out of FileChooser into its own class for more generic usage, and extra data safe-guarding functionality
Ben Soares [Mon, 22 Oct 2018 16:03:15 +0000 (17:03 +0100)]
JAL-3141 Taken the backing up code out of FileChooser into its own class for more generic usage, and extra data safe-guarding functionality
Ben Soares [Mon, 22 Oct 2018 09:25:09 +0000 (10:25 +0100)]
JAL-3141 Tidying
Ben Soares [Fri, 19 Oct 2018 16:26:27 +0000 (17:26 +0100)]
JAL-3141 Backup files being created with default suffix up to 10 backups. Configurable in .jalview_properties but no GUI for this yet.
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
git://source.jalview.org / jalview.git / log