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
gmungoc [Fri, 18 Jan 2019 09:59:45 +0000 (09:59 +0000)]
JAL-3143 'id' not 'ID' attribute drives generation of variant link
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 [Tue, 8 Jan 2019 11:41:22 +0000 (11:41 +0000)]
JAL-3180 Disabled 'By Annotation' group colour menu item
gmungoc [Fri, 4 Jan 2019 16:29:28 +0000 (16:29 +0000)]
JAL-3180 fix By Annotation selection state in colour menu
gmungoc [Fri, 4 Jan 2019 10:32:21 +0000 (10:32 +0000)]
JAL-3181 refactor: extracted buildLinkMenu() for testability
gmungoc [Fri, 4 Jan 2019 08:19:36 +0000 (08:19 +0000)]
JAL-3181 simplified code and test
gmungoc [Thu, 3 Jan 2019 17:11:02 +0000 (17:11 +0000)]
JAL-3181 order link menu items
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 15:11:05 +0000 (15:11 +0000)]
JAL-2621 Overview uses hand cursor in drag box, crosshair outside box
gmungoc [Wed, 19 Dec 2018 14:34:28 +0000 (14:34 +0000)]
JAL-3178 include non-positional features in their group on export
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
Ben Soares [Tue, 18 Dec 2018 14:14:57 +0000 (14:14 +0000)]
JAL-3130 added a javac helper script too (like the java helper script)
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 16:30:13 +0000 (16:30 +0000)]
Merge branch 'develop' into bug/JAL-2830_editManglesDatasetSequence
Jim Procter [Mon, 17 Dec 2018 16:30:06 +0000 (16:30 +0000)]
JAL-2830 reinstate toUppercase for new dataset sequences synthesised during edits.
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
Ben Soares [Mon, 17 Dec 2018 10:37:13 +0000 (10:37 +0000)]
JAL-3130 java bash wrapper to choose which java to run (if this is first in path) -- useful when you want javac and java to be from different JAVA_HOME when running ant
Ben Soares [Mon, 17 Dec 2018 10:34:21 +0000 (10:34 +0000)]
JAL-3130 Some fixes to ant build xml, and the modules list file creation (to remove trailing newline) so it can be used with module-less AdoptOpenJDK barebones JRE
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
Ben Soares [Fri, 14 Dec 2018 10:10:39 +0000 (10:10 +0000)]
JAL-3130 single class testing on CLI with ant [ -Dclass.name=path/from/classpath/to/Test.class ], and 'fixed' some other tests [that I broke]
Ben Soares [Thu, 13 Dec 2018 14:50:02 +0000 (14:50 +0000)]
JAL-3130 Fixing a few more tests that pass on a Mac but not on linux (e.g. jv-bamboo)
Ben Soares [Thu, 13 Dec 2018 12:12:21 +0000 (12:12 +0000)]
JAL-3130 Use non-deprecated check for Mac CMD key press
Ben Soares [Thu, 13 Dec 2018 09:27:46 +0000 (09:27 +0000)]
JAL-3130 Attempting to fix 8 tests that pass on a Mac but not on linux (e.g. jv-bamboo)
Ben Soares [Tue, 11 Dec 2018 17:09:51 +0000 (17:09 +0000)]
JAL-3130 Turns out Quit/About/Preferences handlers are Mac specific, d'oh. Moved build.xml to build-j11.xml
Ben Soares [Mon, 10 Dec 2018 16:59:56 +0000 (16:59 +0000)]
JAL-3130 another tweak for bamboo to add the JDK jmods to --module-path
Ben Soares [Mon, 10 Dec 2018 15:59:59 +0000 (15:59 +0000)]
JAL-3130 build.xml tweaks for clover-3.4.1
gmungoc [Mon, 10 Dec 2018 12:09:43 +0000 (12:09 +0000)]
JAL-1421 added type to List and Vector
gmungoc [Mon, 10 Dec 2018 11:25:44 +0000 (11:25 +0000)]
JAL-3169 leave file browser open on Cancel in overwrite check
Ben Soares [Mon, 10 Dec 2018 11:01:49 +0000 (11:01 +0000)]
JAL-3130 tweaked build.xml to do java 11 bytecode compiling[git branchgit branch]. updated getJavaVersion and added showJDKVersion in utils.
Ben Soares [Fri, 7 Dec 2018 10:26:10 +0000 (10:26 +0000)]
JAL-3130 Some re-reorganisation for build process
Ben Soares [Thu, 6 Dec 2018 16:29:24 +0000 (16:29 +0000)]
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor and new script utils/jdeps_jlink_all.sh which works out module dependencies (not as straightforward as it should be) and makes a java 11 JRE
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
Ben Soares [Mon, 3 Dec 2018 15:18:17 +0000 (15:18 +0000)]
JAL-3130 de-multi-release-jar.sh Script to make multi-release jar file single release.
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 [Mon, 3 Dec 2018 12:20:57 +0000 (12:20 +0000)]
JAL-3130 Added flagged runtime 'Reflection' check on Java9 Quit/About/Preferences Handlers
Ben Soares [Fri, 30 Nov 2018 16:54:00 +0000 (16:54 +0000)]
JAL-3130 refactored a lot of this. See the JAVA-11-README
gmungoc [Fri, 30 Nov 2018 10:26:22 +0000 (10:26 +0000)]
JAL-2420 don't offer Reveal All over alignment panel
gmungoc [Fri, 30 Nov 2018 10:15:11 +0000 (10:15 +0000)]
JAL-3166 catch NPE if all sequences are hidden
gmungoc [Thu, 29 Nov 2018 15:05:56 +0000 (15:05 +0000)]
JAL-3140 updated IntervalStore jar
gmungoc [Thu, 29 Nov 2018 10:04:24 +0000 (10:04 +0000)]
JAL-3140 named tagged version of intervalstore.jar
gmungoc [Thu, 29 Nov 2018 09:42:43 +0000 (09:42 +0000)]
JAL-3140 NCList now via IntervalStore library