Ben Soares [Wed, 22 Apr 2020 19:18:27 +0000 (20:18 +0100)]
JAL-3608 non-JS cherry-pick
Cleaned up Look and Feel selection and enabled specific selections via "laf" property or .jalview_properties property "PREFERRED_LAF".
Default behaviour is the same as before for all platforms except Linux which will now always default to "Metal" (ignoring the property 'swing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel' that is set by the system in Ubuntu [and plausibly other OSes, though not Kubuntu]). If a laf property is set then this obviously gets used if possible.
Also added an optional gradle 'testLaf' property (e.g. gradle -PtestLaf=metal test) which will set the laf property during tests. Possibly handy to spot differences to test results between mac and build server (which will default to Metal).
Recognised values of "laf" are:
(specific LaFs) "metal", "gtk", "quaqua", "vaqua", "nimbus",
(best guess LaFs) "mac", "system", "crossplatform"
Ben Soares [Tue, 16 Jun 2020 12:51:05 +0000 (13:51 +0100)]
JAL-3608 formatting save only
Ben Soares [Tue, 16 Jun 2020 12:49:33 +0000 (13:49 +0100)]
JAL-3608 formatting save only
gmungoc [Mon, 18 May 2020 08:39:55 +0000 (09:39 +0100)]
JAL-3613 remove debug code committed in error
gmungoc [Fri, 1 May 2020 11:41:00 +0000 (12:41 +0100)]
Merge branch 'bug/JAL-3613emblCDSTracking' into releases/Release_2_11_1_Branch
gmungoc [Fri, 1 May 2020 11:36:58 +0000 (12:36 +0100)]
JAL-3613 check sequence overlap when matching search results
Jim Procter [Tue, 21 Apr 2020 23:07:33 +0000 (00:07 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 23:07:21 +0000 (00:07 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 23:06:07 +0000 (00:06 +0100)]
JAL-3407 add GPL license to Jalview source files
Jim Procter [Tue, 21 Apr 2020 23:03:25 +0000 (00:03 +0100)]
JAL-3407 release notes - JAL-247 - for auto-set-ID, and revise wording for transferring virtual features in chimera
Jim Procter [Tue, 21 Apr 2020 20:19:35 +0000 (21:19 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 20:19:16 +0000 (21:19 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 20:18:56 +0000 (21:18 +0100)]
JAL-3407 fix JAL-3574 - remove from known issues for 2.11.1.0
Jim Procter [Tue, 21 Apr 2020 17:23:57 +0000 (18:23 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 17:23:46 +0000 (18:23 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 17:23:11 +0000 (18:23 +0100)]
JAL-3574 JAL-3407 release notes
Jim Procter [Tue, 21 Apr 2020 17:06:17 +0000 (18:06 +0100)]
Merge branch 'bug/JAL-3574filterByPOS' into documentation/JAL-3407_2.11.1_release
Jim Procter [Tue, 21 Apr 2020 17:04:40 +0000 (18:04 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 17:04:33 +0000 (18:04 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 17:03:45 +0000 (18:03 +0100)]
Merge branch 'documentation/JAL-3407_2.11.1_release' into develop
Jim Procter [Tue, 21 Apr 2020 16:39:33 +0000 (17:39 +0100)]
JAL-3407 add and document ComputePeptideVariants.groovy
Ben Soares [Tue, 21 Apr 2020 14:37:32 +0000 (15:37 +0100)]
JAL-3577 changed default RELEASE dir in build.gradle to use absolute path to help buildship when importing project for first time
Jim Procter [Tue, 21 Apr 2020 13:16:50 +0000 (14:16 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 13:16:17 +0000 (14:16 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 21 Apr 2020 13:15:07 +0000 (14:15 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 21 Apr 2020 13:10:22 +0000 (14:10 +0100)]
JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April
Ben Soares [Tue, 21 Apr 2020 11:07:53 +0000 (12:07 +0100)]
JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list
Jim Procter [Tue, 21 Apr 2020 10:58:30 +0000 (11:58 +0100)]
Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop
Jim Procter [Tue, 21 Apr 2020 10:48:44 +0000 (11:48 +0100)]
JAL-367 code tidy
Jim Procter [Tue, 21 Apr 2020 10:48:35 +0000 (11:48 +0100)]
JAL-3567 translated rather than imputed peptide
gmungoc [Fri, 17 Apr 2020 13:00:10 +0000 (14:00 +0100)]
JAL-3567 unit tests for linked feature tooltips
gmungoc [Thu, 16 Apr 2020 17:43:21 +0000 (18:43 +0100)]
JAL-3567 adjust layout of linked feature report, unit test
gmungoc [Thu, 16 Apr 2020 16:37:46 +0000 (17:37 +0100)]
JAL-3567 added 'imputed by Jalview' to protein consequence in report
gmungoc [Thu, 16 Apr 2020 15:11:23 +0000 (16:11 +0100)]
JAL-3567 report mapped location for virtual features in tooltip etc
Jim Procter [Tue, 14 Apr 2020 15:39:04 +0000 (16:39 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 14 Apr 2020 15:38:39 +0000 (16:38 +0100)]
JAL-3407 JAL-3529 release notes
Jim Procter [Tue, 14 Apr 2020 15:33:50 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-3529_uniprotidsinstockholm' into develop
Jim Procter [Tue, 14 Apr 2020 15:33:22 +0000 (16:33 +0100)]
JAL-3529 revert ordering of DBRef addition so it reflects situation after Pfam import </picky>
Jim Procter [Tue, 14 Apr 2020 15:09:51 +0000 (16:09 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 14 Apr 2020 12:50:54 +0000 (13:50 +0100)]
JAL-3597 improved Memory test suite by detecting base memory usage rather than assuming it is constant for each release.
Jim Procter [Tue, 14 Apr 2020 12:24:46 +0000 (13:24 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 14 Apr 2020 12:21:38 +0000 (13:21 +0100)]
JAL-3407 release date set to 16th April, known issue report for JAL-3574
Jim Procter [Tue, 14 Apr 2020 11:25:20 +0000 (12:25 +0100)]
Merge branch 'testing/JAL-3577_jalviewversion_autoset_fixed' into develop
gmungoc [Mon, 13 Apr 2020 15:42:42 +0000 (16:42 +0100)]
JAL-3574 test coverage corners
gmungoc [Mon, 13 Apr 2020 11:45:38 +0000 (12:45 +0100)]
JAL-3574 Matcher with integer/long value pattern (e.g. VCF POS locus)
gmungoc [Sun, 12 Apr 2020 14:43:21 +0000 (15:43 +0100)]
JAL-3596 change redacted
gmungoc [Sun, 12 Apr 2020 12:24:24 +0000 (13:24 +0100)]
JAL-3596 don't draw text over features if Show Text is unselected
Ben Soares [Thu, 9 Apr 2020 13:32:03 +0000 (14:32 +0100)]
JAL-3588 Remove Examples folder in windows Program Group for all CHANNEL values
Jim Procter [Thu, 9 Apr 2020 11:04:07 +0000 (12:04 +0100)]
JAL-3577 automatically configure JALVIEW_VERSION for builds using jalview.version property in RELEASE file
Ben Soares [Tue, 7 Apr 2020 13:24:02 +0000 (14:24 +0100)]
JAL-3577 improvement to non-release DMG background and source SVG. Updated docs on image specification/creation.
Ben Soares [Tue, 7 Apr 2020 00:30:12 +0000 (01:30 +0100)]
Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop
Ben Soares [Tue, 7 Apr 2020 00:29:33 +0000 (01:29 +0100)]
JAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling
Ben Soares [Mon, 6 Apr 2020 21:34:06 +0000 (22:34 +0100)]
JAL-3577 Fixed Jalview Programme Group in Windows menu. Added examples folder for RELEASE channel only and Examples folder in Jalview Programme Group in Windows.
Jim Procter [Mon, 6 Apr 2020 16:48:32 +0000 (17:48 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 6 Apr 2020 16:47:45 +0000 (17:47 +0100)]
JAL-3407 redact java 8 incompatible type inference
Jim Procter [Mon, 6 Apr 2020 16:27:29 +0000 (17:27 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 6 Apr 2020 16:25:35 +0000 (17:25 +0100)]
JAL-3407 updated release date to Thursday 9th April, and release notes for JAL-3577 JAL-3581 JAL-3571
gmungoc [Mon, 6 Apr 2020 14:58:33 +0000 (15:58 +0100)]
JAL-3581 no hidden sequence marker if hidden markers not shown
Ben Soares [Mon, 6 Apr 2020 14:49:30 +0000 (15:49 +0100)]
JAL-3577 Moved application Categories for freedesktop menus into correct place in install4j
Ben Soares [Mon, 6 Apr 2020 12:32:30 +0000 (13:32 +0100)]
JAL-3577 removed debugging
Ben Soares [Mon, 6 Apr 2020 12:29:40 +0000 (13:29 +0100)]
Merge branch 'task/JAL-3577_Jalview_Test_installers' into develop
Ben Soares [Mon, 6 Apr 2020 12:27:56 +0000 (13:27 +0100)]
JAL-3577 Added existing and new Application IDs for Windows. Fixed Desktop shortcut and Menu entry.
gmungoc [Mon, 6 Apr 2020 09:18:17 +0000 (10:18 +0100)]
JAL-3579 no Feature Editor if features not shown
Jim Procter [Mon, 6 Apr 2020 08:20:49 +0000 (09:20 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Ben Soares [Mon, 6 Apr 2020 08:20:35 +0000 (09:20 +0100)]
JAL-3577 Changed shortName to INTERNAL_ID
Ben Soares [Sun, 5 Apr 2020 09:50:46 +0000 (10:50 +0100)]
JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'
Ben Soares [Sun, 5 Apr 2020 09:50:12 +0000 (10:50 +0100)]
JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'
Ben Soares [Sat, 4 Apr 2020 00:01:39 +0000 (01:01 +0100)]
JAL-3577 Added DS_Store for Test release to look like proper installer
Ben Soares [Fri, 3 Apr 2020 16:04:30 +0000 (17:04 +0100)]
JAL-3577 Added a jalviewt scheme ONLY to TEST-RELEASE and TEST-LOCAL channels so that a test jvl can be made to ONLY open in the Test installation
Ben Soares [Fri, 3 Apr 2020 15:44:56 +0000 (16:44 +0100)]
JAL-3577 cleaned up old DMG files. Added NON-RELEASE DMG files. Changed how Jalview name propogates through install4j -- now dynamically created depending on the CHANNEL
Ben Soares [Thu, 2 Apr 2020 23:41:49 +0000 (00:41 +0100)]
JAL-3577 First attempt at new folder names
Jim Procter [Thu, 2 Apr 2020 16:11:10 +0000 (17:11 +0100)]
Merge branch 'develop' into releases/Release_2_11_1_Branch
Ben Soares [Thu, 2 Apr 2020 13:55:22 +0000 (14:55 +0100)]
JAL-3572 Added getdown Implementation-Version to getdown jars META-INF/MANIFEST.MF
Ben Soares [Thu, 2 Apr 2020 11:42:30 +0000 (12:42 +0100)]
Merge branch 'improvement/JAL-3394_added_categories_to_unix_shell_installer_desktop_file' into develop
Jim Procter [Tue, 31 Mar 2020 22:15:32 +0000 (23:15 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 31 Mar 2020 22:10:44 +0000 (23:10 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into develop
Jim Procter [Tue, 31 Mar 2020 22:09:42 +0000 (23:09 +0100)]
JAL-3407 basic doc for releasing jalview - will be embellished as we go
Jim Procter [Tue, 31 Mar 2020 21:54:41 +0000 (22:54 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Jim Procter [Tue, 31 Mar 2020 21:53:24 +0000 (22:53 +0100)]
JAL-3407 updated release date to 2nd April, and first draft of release notes
gmungoc [Tue, 31 Mar 2020 13:41:15 +0000 (14:41 +0100)]
JAL-1889 better (?) wait for Conservation thread
Jim Procter [Tue, 31 Mar 2020 09:25:54 +0000 (10:25 +0100)]
Merge branch 'documentation/Release_2_11_1_Branch' into develop
Jim Procter [Mon, 30 Mar 2020 17:03:30 +0000 (18:03 +0100)]
JAL-3407 2.11.1.0 release date bump - maybe tomorrow - maybe the next day !
Jim Procter [Mon, 30 Mar 2020 17:03:09 +0000 (18:03 +0100)]
JAL-3407 JAL-3130 back out java 9+ syntax that breaks java 8 builds
soares [Fri, 27 Mar 2020 16:08:13 +0000 (16:08 +0000)]
JAL-3225 updated essential files for eclipse project if buildship fails
Ben Soares [Thu, 26 Mar 2020 20:22:52 +0000 (20:22 +0000)]
JAL-3225 Also look for local.properties in file named ../${projectDir}_local.properties. This allows multiple instances of the same project in Eclipse by changing the eclipse_project_name propert (and other local properties)
soares [Thu, 26 Mar 2020 17:37:44 +0000 (17:37 +0000)]
JAL-3225 This one file needed for project if git clean -dfx run
Ben Soares [Thu, 26 Mar 2020 17:13:40 +0000 (17:13 +0000)]
JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs
Ben Soares [Wed, 25 Mar 2020 17:07:36 +0000 (17:07 +0000)]
JAL-3248 Added instructions for downloading and configuring as gradle project in Eclipse only, i.e. no command line tools needed
Jim Procter [Fri, 20 Mar 2020 18:19:52 +0000 (18:19 +0000)]
JAL-3562 exclude testNG groups from a build via -PtestngExcludedGroups=Not-bamboo
Jim Procter [Fri, 20 Mar 2020 18:01:57 +0000 (18:01 +0000)]
JAL-3407 JAL-3562 release notes
Jim Procter [Fri, 20 Mar 2020 17:50:47 +0000 (17:50 +0000)]
JAL-3407 rejigging new features - simplify release note line for virtual features
Jim Procter [Fri, 20 Mar 2020 17:45:08 +0000 (17:45 +0000)]
JAL-3407 reformat releases.html
Jim Procter [Fri, 20 Mar 2020 17:27:01 +0000 (17:27 +0000)]
JAL-3407 JAL-3549 javadoc
Jim Procter [Fri, 20 Mar 2020 17:02:49 +0000 (17:02 +0000)]
JAL-3407 - release notes for JAL-3547
Jim Procter [Fri, 20 Mar 2020 17:01:53 +0000 (17:01 +0000)]
JAL-3549 javadoc
gmungoc [Thu, 19 Mar 2020 16:05:57 +0000 (16:05 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Ben Soares [Thu, 19 Mar 2020 12:54:02 +0000 (12:54 +0000)]
JAL-3541 increase maxheapsize for test worker process
Ben Soares [Thu, 19 Mar 2020 12:35:45 +0000 (12:35 +0000)]
JAL-3541 tidying build.gradle, delete cloverInstrDir re-added
gmungoc [Thu, 19 Mar 2020 12:29:46 +0000 (12:29 +0000)]
JAL-3305 don't propagate an empty SelectionGroup to complement view
Ben Soares [Thu, 19 Mar 2020 12:26:41 +0000 (12:26 +0000)]
JAL-3541 put org.gradle.jvmargs explicitly into gradle.properties
git://source.jalview.org / jalview.git / log