Ben Soares [Wed, 3 Jul 2019 13:03:30 +0000 (14:03 +0100)]
JAL-3349 Remove processed args from list to send to jalview
Ben Soares [Wed, 3 Jul 2019 13:02:14 +0000 (14:02 +0100)]
JAL-3349 Added a prefix for cli args to getdown that get turned into JVM args for Jalview. Also a -jvmmempc lookup
Ben Soares [Wed, 3 Jul 2019 00:36:50 +0000 (01:36 +0100)]
JAL-3348 prepping getdown to pass JVM command line args
Jim Procter [Tue, 2 Jul 2019 20:21:09 +0000 (21:21 +0100)]
JAL-3111 fix broken helpTOC link
Jim Procter [Tue, 2 Jul 2019 20:19:46 +0000 (21:19 +0100)]
Merge branch 'tasks/JAL-3311_removeVamsasMenu' into develop
Jim Procter [Tue, 2 Jul 2019 19:47:52 +0000 (20:47 +0100)]
Merge branch 'develop' into tasks/JAL-3311_removeVamsasMenu
Jim Procter [Tue, 2 Jul 2019 15:06:55 +0000 (16:06 +0100)]
JAL-3111 release date now 4th July 2019 - codename 'bastille'
Jim Procter [Tue, 2 Jul 2019 14:34:10 +0000 (15:34 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Tue, 2 Jul 2019 14:33:20 +0000 (15:33 +0100)]
JAL-3111 formatting
Jim Procter [Tue, 2 Jul 2019 14:32:53 +0000 (15:32 +0100)]
JAL-3111 new known defect from JAL-797
Jim Procter [Tue, 2 Jul 2019 14:30:11 +0000 (15:30 +0100)]
JAL-3111 release notes for JAL-2789 JAL-2744 JAL-1889 JAL-3287 JAL-3289 JAL-3288
Jim Procter [Tue, 2 Jul 2019 14:28:19 +0000 (15:28 +0100)]
JAL-3111 whats new and JAL-2738 JAL-2743 expanded help documentation for VCF
Ben Soares [Mon, 1 Jul 2019 23:07:23 +0000 (00:07 +0100)]
JAL-3322 increase concurrent downloads in getdown
Ben Soares [Mon, 1 Jul 2019 15:40:37 +0000 (16:40 +0100)]
JAL-3333 removed unused variable
Ben Soares [Mon, 1 Jul 2019 14:35:30 +0000 (15:35 +0100)]
JAL-3322 getdown jars with network timeouts applied
Ben Soares [Mon, 1 Jul 2019 14:21:00 +0000 (15:21 +0100)]
JAL-3332 Sensible default timeout values for network connections (8s connect_timeout, 15s read_timeout)
Ben Soares [Mon, 1 Jul 2019 11:27:01 +0000 (12:27 +0100)]
JAL-3333 using floats for smoother weighting
Ben Soares [Sat, 29 Jun 2019 12:48:25 +0000 (13:48 +0100)]
JAL-3333 Sorry couldn't resist adding a bit of weighting to the rotation
Ben Soares [Sat, 29 Jun 2019 00:52:43 +0000 (01:52 +0100)]
JAL-3333 Title text now appears instantly. Altering speed of rotating logo depending on queuing or running status. Rotating logo now 'parks' rather than jumps at completion.
Ben Soares [Fri, 28 Jun 2019 16:27:40 +0000 (17:27 +0100)]
Merge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceInfo_window_title_in_macOS_mojave' into develop
Merging in simple change from transparent image to white background and removing alpha channel in image model.
Ben Soares [Fri, 28 Jun 2019 16:27:03 +0000 (17:27 +0100)]
JAL-3333 changed RGB model. Tested in mojave and Windows (works)
Jim Procter [Fri, 28 Jun 2019 16:08:30 +0000 (17:08 +0100)]
JAL-3111 release notes for JAL-3330 JAL-3021 (tweak) and JAL-3333
Jim Procter [Fri, 28 Jun 2019 15:30:02 +0000 (16:30 +0100)]
Merge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceInfo_window_title_in_macOS_mojave' into develop
Jim Procter [Fri, 28 Jun 2019 15:29:07 +0000 (16:29 +0100)]
JAL-3111 release notes for JAL-2820 JAL-2207
Jim Procter [Fri, 28 Jun 2019 15:28:43 +0000 (16:28 +0100)]
JAL-3111 backed out report of fix to JAL-3178 in release notes - since not fixed for 2.11
Jim Procter [Fri, 28 Jun 2019 15:27:55 +0000 (16:27 +0100)]
JAL-3111 JAL-3340 JAL-3184 JAL-3338 new known defects
Ben Soares [Fri, 28 Jun 2019 14:54:01 +0000 (15:54 +0100)]
JAL-3333 Smooth rotation of image now too
Jim Procter [Fri, 28 Jun 2019 14:12:39 +0000 (15:12 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Fri, 28 Jun 2019 14:12:09 +0000 (15:12 +0100)]
JAL-3111 final release date for 2.11.0
Ben Soares [Fri, 28 Jun 2019 14:05:19 +0000 (15:05 +0100)]
JAL-3333 added height to rotating image preferred size
Jim Procter [Fri, 28 Jun 2019 13:17:54 +0000 (14:17 +0100)]
JAL-3330 apply Ensembl feature settings when showing crossrefs for alignment that looks like it was from Ensembl
Ben Soares [Fri, 28 Jun 2019 13:09:32 +0000 (14:09 +0100)]
JAL-3333 Replaced title text rendered in animated image with a titleText JLabel. Moved image to WEST with preferred size and put titleText in CENTER.
Ben Soares [Fri, 28 Jun 2019 11:05:32 +0000 (12:05 +0100)]
JAL-3335 much improved getdown background images
Ben Soares [Fri, 28 Jun 2019 09:41:45 +0000 (10:41 +0100)]
JAL-3322 Progress bar status tweaks
Ben Soares [Fri, 28 Jun 2019 09:37:58 +0000 (10:37 +0100)]
JAL-3322 getdown Application class fix
Ben Soares [Fri, 28 Jun 2019 09:33:48 +0000 (10:33 +0100)]
Merge branch 'develop' into JAL-3322_getdown_speed_improvement
merging in develop
Ben Soares [Fri, 28 Jun 2019 09:33:18 +0000 (10:33 +0100)]
JAL-3322 corrected fix to convertBuildingMD task fail. removed debugging warnings from getdown config backups
Ben Soares [Fri, 28 Jun 2019 07:59:34 +0000 (08:59 +0100)]
Merge branch 'JAL-3322_getdown_speed_improvement' of https://source.jalview.org/git/jalview into JAL-3322_getdown_speed_improvement
parallel dev
Ben Soares [Thu, 27 Jun 2019 22:29:54 +0000 (23:29 +0100)]
JAL-3322 fixed convertBuildingMD task skipping in Windows
Jim Procter [Thu, 27 Jun 2019 16:04:14 +0000 (17:04 +0100)]
Merge branch 'JAL-3322_getdown_speed_improvement' into develop
Ben Soares [Thu, 27 Jun 2019 13:42:56 +0000 (14:42 +0100)]
JAL-3322 linksCheck task output.
Ben Soares [Thu, 27 Jun 2019 12:02:54 +0000 (13:02 +0100)]
JAL-3322 Removed debug logging. Enabled backup install/getdown.txt config. Added a dev doc diagram.
Ben Soares [Wed, 26 Jun 2019 23:55:20 +0000 (00:55 +0100)]
JAL-3322 Once background displayed, allow asynchronous progress setting
Ben Soares [Wed, 26 Jun 2019 23:25:48 +0000 (00:25 +0100)]
JAL-3111 fixed an anchor name link preventing linkCheck task from completing successfully
Jalview Development Admin [Wed, 26 Jun 2019 17:25:30 +0000 (18:25 +0100)]
JAL-3111 sign the uninstaller script .. again
Jim Procter [Wed, 26 Jun 2019 17:20:55 +0000 (18:20 +0100)]
Merge branch 'improvement/JAL-3322_getdown_splashscreen_visibility' into develop
also note JAL-3320 addressed (groovy console opening with Java 11)
Jim Procter [Wed, 26 Jun 2019 17:16:46 +0000 (18:16 +0100)]
Merge branch 'develop' into improvement/JAL-3322_getdown_splashscreen_visibility
Jim Procter [Wed, 26 Jun 2019 17:07:41 +0000 (18:07 +0100)]
JAL-3111 release notes for JAL-3334 JAL-3330 and rejig others
Jim Procter [Wed, 26 Jun 2019 16:49:33 +0000 (17:49 +0100)]
Merge branch 'bug/JAL-3330' into develop
Jim Procter [Wed, 26 Jun 2019 16:43:34 +0000 (17:43 +0100)]
JAL-3334 fix - always load full SO to resolve the sequence features from Ensembl correctly
Jim Procter [Wed, 26 Jun 2019 16:37:57 +0000 (17:37 +0100)]
JAL-3111 get rid of nasty tab characters
Jim Procter [Wed, 26 Jun 2019 16:36:58 +0000 (17:36 +0100)]
JAL-3332 test to check for duplicate db sources and patch to code. crept in after das source removal
Ben Soares [Wed, 26 Jun 2019 16:13:35 +0000 (17:13 +0100)]
JAL-3130 Added all groovy jars for groovy console
Ben Soares [Wed, 26 Jun 2019 15:33:37 +0000 (16:33 +0100)]
Merge branch 'develop' into improvement/JAL-3322_getdown_splashscreen_visibility
merging with develop
Ben Soares [Wed, 26 Jun 2019 14:50:06 +0000 (15:50 +0100)]
JAL-3322 Splashcreen now appears instantly with new setting ui.progress_sync = true. Some other minor improvements
Jim Procter [Wed, 26 Jun 2019 11:08:49 +0000 (12:08 +0100)]
JAL-3330 JAL-3332 relocate and simplify BeforeClass/BeforeTest to avoid ambiguity in setup
Jim Procter [Wed, 26 Jun 2019 10:55:26 +0000 (11:55 +0100)]
JAL-3330 test to verify sub/attributeName array is not shared between multiple instances after copy-via-copy constructor
Jim Procter [Wed, 26 Jun 2019 10:53:56 +0000 (11:53 +0100)]
JAL-3330 javadoc
Ben Soares [Tue, 25 Jun 2019 16:04:12 +0000 (17:04 +0100)]
JAL-3322 replaced invokeAndWait(r) with r.run() and fixed nullpointer error in jvl config reading
Ben Soares [Tue, 25 Jun 2019 15:16:13 +0000 (16:16 +0100)]
JAL-3289 Ehancements to ARCHIVE building and script to show how to batch build and rsync the archived versions
Ben Soares [Tue, 25 Jun 2019 11:50:35 +0000 (12:50 +0100)]
JAL-3289 ARCHIVE now implemented (requires a compiled -PARCHIVEDIST=/path/to/old/jalview/dist). Improved delete file values in uninstaller. Added an ARCHIVELOCAL channel type for testing.
Ben Soares [Mon, 24 Jun 2019 20:20:08 +0000 (21:20 +0100)]
JAL-3289 implemented CHANNEL=LOCAL,RELEASE,TEST-RELEASE,SCRATCHH-...,DEVELOP,ARCHIVE. Added fallback install/getdown-launcher.jar and added to classpath in install4j_template.install4j
Jim Procter [Mon, 24 Jun 2019 17:37:52 +0000 (18:37 +0100)]
JAL-3330 merge styles onto originating view after fetching database references
Jim Procter [Mon, 24 Jun 2019 17:36:54 +0000 (18:36 +0100)]
JAL-3330 dbreffetcher: record any feature display models associated with sources that provide sequences
Jim Procter [Mon, 24 Jun 2019 17:36:04 +0000 (18:36 +0100)]
JAL-3330 merge styles onto originating views when show cross-refs performed (should really do this for all views involving dataset).
Jim Procter [Mon, 24 Jun 2019 16:43:33 +0000 (17:43 +0100)]
JAL-3330 mergeFeatureStyles - needs test coverage
Ben Soares [Mon, 24 Jun 2019 14:59:07 +0000 (15:59 +0100)]
JAL-3322 improve visibility of versioning of launcher
Jim Procter [Mon, 24 Jun 2019 13:31:48 +0000 (14:31 +0100)]
JAL-3111 formatting
Jim Procter [Mon, 24 Jun 2019 12:59:59 +0000 (13:59 +0100)]
JAL-3111 JAL-2069 JAL-2808 documentation for feature filters and enhanced feature colours. Revised feature settings documentation for legibility.
Ben Soares [Mon, 24 Jun 2019 00:38:18 +0000 (01:38 +0100)]
JAL-3289 Start looking at automating location in appbase more sensibly
Ben Soares [Sat, 22 Jun 2019 09:14:39 +0000 (10:14 +0100)]
JAL-3328 improvement to the EQinvoke code
Ben Soares [Fri, 21 Jun 2019 22:37:27 +0000 (23:37 +0100)]
JAL-3328 Made choice of invokeLater or invokeAndWait configurable
Jim Procter [Fri, 21 Jun 2019 16:27:30 +0000 (17:27 +0100)]
JAL-3111 added Colour By ID and an overview of Jalview’s alignment colouring capabilities
Ben Soares [Fri, 21 Jun 2019 16:15:19 +0000 (17:15 +0100)]
JAL-3328 JAL-3300 changed invokeLaters to invokeAndWaits for more visible progress
Ben Soares [Fri, 21 Jun 2019 13:56:01 +0000 (14:56 +0100)]
JAL-3328 Getdown version number, changed to 1.8.3-1.0_JVL
Ben Soares [Fri, 21 Jun 2019 13:55:12 +0000 (14:55 +0100)]
JAL-3328 Improved progress bar. Higher-res file icons. Splashscreen visibile for slightly longer (now at least 7 seconds).
Ben Soares [Fri, 21 Jun 2019 09:01:30 +0000 (10:01 +0100)]
JAL-3322 Adding a configurable getdown version number display (above appbase) to getdown splashscreen
Ben Soares [Fri, 21 Jun 2019 07:53:01 +0000 (08:53 +0100)]
Merge branch 'develop' into improvement/JAL-3322_getdown_splashscreen_visibility
merging in develop
Jim Procter [Thu, 20 Jun 2019 16:48:08 +0000 (17:48 +0100)]
JAL-3111 JAL-2962 JAL-2903 JAL-2986 release notes
Jim Procter [Thu, 20 Jun 2019 16:10:42 +0000 (17:10 +0100)]
JAL-3111 last final release date for 2.11.0 !
Jim Procter [Thu, 20 Jun 2019 16:10:28 +0000 (17:10 +0100)]
JAL-3111 2.11 improvement JAL-3205 JAL-3203
Post-hoc documentation of known defects not listed in earlier versions.
Ben Soares [Thu, 20 Jun 2019 16:00:18 +0000 (17:00 +0100)]
JAL-3322 New progress bar. Added option to report appbase in launcher window. Added ui.keep_on_top option for getdown window. Added a launch.jvl file. Added build_properties as a resource and build_properties.install at installation time (only)
Jim Procter [Thu, 20 Jun 2019 15:10:13 +0000 (16:10 +0100)]
JAL-3111 JAL-1424 release notes
Jim Procter [Thu, 20 Jun 2019 14:02:59 +0000 (15:02 +0100)]
JAL-3111 JAL-2816 docs
Jim Procter [Thu, 20 Jun 2019 13:47:33 +0000 (14:47 +0100)]
JAL-3111 signed off ’done’ issues in Jira as of now:
JAL-1059,JAL-1117,JAL-1285,JAL-1793,JAL-1839,JAL-1929,JAL-2069,JAL-2185,JAL-2360,JAL-2416,JAL-2446,JAL-2620,JAL-2647,JAL-2671,JAL-2729,JAL-2753,JAL-2808,JAL-2816,JAL-2839,JAL-2864,JAL-2886,JAL-2898,JAL-2932,JAL-2965,JAL-3007,JAL-3018,JAL-3021,JAL-3139,JAL-3140,JAL-3141,JAL-3174,JAL-3179,JAL-3196,JAL-3198,JAL-3225,JAL-3232,JAL-3236,JAL-3248,JAL-3254,JAL-3260,JAL-3313,JAL-781,JAL-868
Jim Procter [Thu, 20 Jun 2019 12:19:16 +0000 (13:19 +0100)]
JAL-3111 JAL-3130 JAL-3235 Java 11 specific known defects in 2.11
Ben Soares [Thu, 20 Jun 2019 11:53:57 +0000 (12:53 +0100)]
JAL-3323 Improved macOS Old Jalview Uninstaller
Jalview Development Admin [Wed, 19 Jun 2019 12:42:49 +0000 (13:42 +0100)]
JAL-3111 codesign the uninstaller again
Ben Soares [Wed, 19 Jun 2019 11:51:21 +0000 (12:51 +0100)]
Merge branch 'merge/JAL-3310_and_JAL-3300' into develop
Ben Soares [Wed, 19 Jun 2019 11:50:36 +0000 (12:50 +0100)]
JAL-3321 Last pieces of the getdown-launcher.jar upgrade puzzle
Ben Soares [Wed, 19 Jun 2019 11:48:30 +0000 (12:48 +0100)]
JAL-3310 Removing i4jruntime.jar from dist. Not needed by Jalview
Jim Procter [Wed, 19 Jun 2019 10:13:34 +0000 (11:13 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 19 Jun 2019 10:12:47 +0000 (11:12 +0100)]
JAL-3111 release notes for JAL-3313
Jim Procter [Wed, 19 Jun 2019 10:09:20 +0000 (11:09 +0100)]
JAL-3111 formatting
Jim Procter [Wed, 19 Jun 2019 10:05:54 +0000 (11:05 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Wed, 19 Jun 2019 10:01:43 +0000 (11:01 +0100)]
JAL-3111 release notes for JAL-27830 JAL-2876 JAL-2567 and JAL-2256
Ben Soares [Wed, 19 Jun 2019 00:29:05 +0000 (01:29 +0100)]
JAL-3321 Corrected the badly configured getdown-launcher.jar for updating and updated build.gradle to make the right getdown.txt file
gmungoc [Tue, 18 Jun 2019 17:06:08 +0000 (18:06 +0100)]
JAL-3313 don't double count mapped codons
Jim Procter [Tue, 18 Jun 2019 16:49:23 +0000 (17:49 +0100)]
Merge branch 'bug/JAL-2830_editManglesDatasetSequence' into develop
Jim Procter [Tue, 18 Jun 2019 15:42:18 +0000 (16:42 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatasetSequence
git://source.jalview.org / jalview.git / log