Ben Soares [Tue, 25 Jun 2024 08:55:45 +0000 (09:55 +0100)]
JAL-3631 Tests for version comparisons and Jar version comparisons and Jar version checking
Ben Soares [Tue, 25 Jun 2024 08:49:23 +0000 (09:49 +0100)]
JAL-3631 Change parity of comparison for convention
Ben Soares [Mon, 24 Jun 2024 23:23:37 +0000 (00:23 +0100)]
JAL-3631 Report getCanonicalPath for installer appdir
Ben Soares [Mon, 24 Jun 2024 23:23:00 +0000 (00:23 +0100)]
JAL-3631 Check Implementation-Version of getdown-launcher.jar in installation appdir and user's appdir, and only use the user one if it's newer. Remove content digest check for getdown-launcher.jar comparison since version now being checked.
Ben Soares [Fri, 21 Jun 2024 17:15:02 +0000 (18:15 +0100)]
JAL-3631 updated getdown jars
Ben Soares [Fri, 21 Jun 2024 15:04:11 +0000 (16:04 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Fri, 21 Jun 2024 15:03:23 +0000 (16:03 +0100)]
JAL-3631 Changed label for consistency
Jim Procter [Fri, 21 Jun 2024 14:26:03 +0000 (15:26 +0100)]
Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into develop
Ben Soares [Fri, 21 Jun 2024 12:49:25 +0000 (13:49 +0100)]
Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Fri, 21 Jun 2024 12:48:41 +0000 (13:48 +0100)]
JAL-4409 Add two empty args to getdown call from install4j for backward compatibility, and further arguments such as JVL file. Improve handling of a JVL file with an appbase in it.
Ben Soares [Fri, 21 Jun 2024 09:00:08 +0000 (10:00 +0100)]
JAL-4409 Don't merge JVL configs when changing appbase
Ben Soares [Thu, 20 Jun 2024 18:27:41 +0000 (19:27 +0100)]
JAL-4409 Use fixed 'latest' artifact URL
Ben Soares [Thu, 20 Jun 2024 17:39:13 +0000 (18:39 +0100)]
JAL-4409 Changes in BUILD channel appbase to tie in with Getdown DEVELOP Launcher build plan
Ben Soares [Thu, 20 Jun 2024 09:12:03 +0000 (10:12 +0100)]
JAL-3631 Now sending launcher.appdir from within getdown
Ben Soares [Wed, 19 Jun 2024 12:35:09 +0000 (13:35 +0100)]
JAL-3631 Rename/rationalise informational system property names. Re-order display of information on Java Console. Supply info from authoratitive sources (getdown-launcher.jar rather than gradle.properties).
Ben Soares [Tue, 18 Jun 2024 22:52:25 +0000 (23:52 +0100)]
JAL-3631 macos dev install script incorporated into dev_install.sh
Ben Soares [Tue, 18 Jun 2024 22:38:09 +0000 (23:38 +0100)]
JAL-4358 slight improvement to detecting desktop creation to close getdown splash screen
Ben Soares [Tue, 18 Jun 2024 20:37:20 +0000 (21:37 +0100)]
JAL-3631 gradle-build-and-re-install script, works with macOS or Linux
Ben Soares [Tue, 18 Jun 2024 20:36:44 +0000 (21:36 +0100)]
JAL-3631 Substantial additions to Getdown (through jalview.util.LaunchUtils) to re-launch getdown-launcher.jar when the user's version differs from the installed version. install4j vmoptions file allows administrator to prevent any automatic updates.
Ben Soares [Mon, 17 Jun 2024 09:45:38 +0000 (10:45 +0100)]
JAL-3631 Allow quick deployment of gradle build on linux and macos
Ben Soares [Fri, 14 Jun 2024 19:53:04 +0000 (20:53 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Fri, 14 Jun 2024 17:51:40 +0000 (18:51 +0100)]
JAL-3631 Got rid of the USER_EXECUTABLE_NAME as it's no longer needed since getting rid of the old Launcher in install4j
Ben Soares [Fri, 14 Jun 2024 17:37:28 +0000 (18:37 +0100)]
JAL-3631 Removed old non-user launcher. Labelled USERSPACE actions.
Ben Soares [Fri, 14 Jun 2024 17:36:45 +0000 (18:36 +0100)]
JAL-3631 JAL-4104 More consistent system property names passing through getdown. Add nousedefaultappdir property to allow non-updating system installation of Jalview.
Ben Soares [Fri, 14 Jun 2024 09:40:37 +0000 (10:40 +0100)]
JAL-3631 Allow -Pinstall4j_build_ids=MACOS-AARCH64-DMG for specific installer build. Fix installer icons (PNGs and paths).
Ben Soares [Thu, 13 Jun 2024 20:20:54 +0000 (21:20 +0100)]
JAL-3845 Add a popup error message, with instructions, when Jalview launched from the Installer Volume
Ben Soares [Thu, 13 Jun 2024 20:20:06 +0000 (21:20 +0100)]
JAL-3631 New Installer icons. Getdown check that the application appdir is different from the user default appdir before copying files. Also copy gedown-launcher.jar.
Ben Soares [Wed, 12 Jun 2024 22:23:03 +0000 (23:23 +0100)]
JAL-3631 Name changes to system properties and a fallback App name to avoid hard-coded name in getdown
Ben Soares [Wed, 12 Jun 2024 22:22:17 +0000 (23:22 +0100)]
JAL-3631 Spot system property triggers in getdown to create/activate using a user-space location (dependent on OS), and copy digest-tested files from the Application's app dir to the user's new app dir. Debugging statements left in for testing on other OSes.
Ben Soares [Wed, 12 Jun 2024 22:18:43 +0000 (23:18 +0100)]
JAL-3631 Add a new launcher in install4j to pass new system properties to getdown, triggering the user-space appdir creation
Ben Soares [Mon, 10 Jun 2024 19:23:13 +0000 (20:23 +0100)]
Merge branch 'bug/JAL-4421_customise_volume_name_of_DMG_installers' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Jim Procter [Mon, 10 Jun 2024 13:18:31 +0000 (14:18 +0100)]
JAL-4159 remove errant jalview source .zip
Ben Soares [Fri, 7 Jun 2024 13:10:14 +0000 (14:10 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Ben Soares [Fri, 7 Jun 2024 11:20:40 +0000 (12:20 +0100)]
JAL-4421 Update the dev_masos_installer.sh to use new Volume name
Ben Soares [Thu, 6 Jun 2024 19:08:18 +0000 (20:08 +0100)]
JAL-4420 Added some more filename extensions
Ben Soares [Thu, 6 Jun 2024 12:54:51 +0000 (13:54 +0100)]
JAL-4072 Add zip-slip check in getdown
Jim Procter [Thu, 6 Jun 2024 10:49:13 +0000 (11:49 +0100)]
Merge branch 'bug/JAL-4421_customise_volume_name_of_DMG_installers' into develop
Ben Soares [Thu, 6 Jun 2024 10:17:41 +0000 (11:17 +0100)]
JAL-4358 Add the JALVIEW: CREATED DESKTOP line to java app and look out for it in Getdown to close the splash screen
Ben Soares [Wed, 5 Jun 2024 20:20:32 +0000 (21:20 +0100)]
JAL-4420 Allow associated files to be dragged on separately from the alignment (but afterwards).
Ben Soares [Wed, 5 Jun 2024 19:39:27 +0000 (20:39 +0100)]
JAL-4409 Small refactoring of ArgParserUtils to allow processFiles to work on drag-and-dropped files list.
Ben Soares [Wed, 5 Jun 2024 14:03:52 +0000 (15:03 +0100)]
Merge branch 'develop' into bug/JAL-4421_customise_volume_name_of_DMG_installers
Ben Soares [Wed, 5 Jun 2024 13:17:38 +0000 (14:17 +0100)]
JAL-4421 Downgrading ds_store to 1.3.0 for build server limitations
Ben Soares [Wed, 5 Jun 2024 00:28:20 +0000 (01:28 +0100)]
JAL-4421 Configuration for positioning icons in DMG
Ben Soares [Wed, 5 Jun 2024 00:27:24 +0000 (01:27 +0100)]
JAL-4421 Add --appname --appxpos --appypos to position variable application name icons, or read from config[app]
Ben Soares [Tue, 4 Jun 2024 20:39:55 +0000 (21:39 +0100)]
JAL-4421 Remove the disk_image_alias from the backgroundImageAlias altogether as it isn't needed and doesn't even make sense for a downloaded DMG
Ben Soares [Tue, 4 Jun 2024 17:35:53 +0000 (18:35 +0100)]
JAL-4421 Allow JSON config file to be options (no icon positioning for default or develop-SUFFIX). Allow .VolumeIcons.icns to be optional -- must remove <file> node from install4j template
Jim Procter [Tue, 4 Jun 2024 15:52:20 +0000 (16:52 +0100)]
Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into develop
Jim Procter [Tue, 4 Jun 2024 15:45:04 +0000 (16:45 +0100)]
JAL-4409 don't ignore gitignore !
Jim Procter [Tue, 4 Jun 2024 15:35:40 +0000 (16:35 +0100)]
JAL-4418 first development release for 2.11.4.0 - release notes for
JAL-4159,JAL-4257,JAL-4386,JAL-4392,JAL-789
Jim Procter [Tue, 4 Jun 2024 15:08:26 +0000 (16:08 +0100)]
Merge branch 'feature/JAL-4159_pasimap' into develop
Conflicts:
help/markdown/releases/release-2_11_3_0.md
Jim Procter [Tue, 4 Jun 2024 15:05:57 +0000 (16:05 +0100)]
Merge branch 'releases/Release_2_11_3_Branch' into develop
Ben Soares [Tue, 4 Jun 2024 00:50:02 +0000 (01:50 +0100)]
JAL-4421 Put correct VolumeIcon.icns file onto DMG volume as /.VolumeIcon.icns
Ben Soares [Mon, 3 Jun 2024 23:50:05 +0000 (00:50 +0100)]
JAL-4421 Icns to use as .VolumeIcon.icns in DMG volumes. See comment with SetFile
Ben Soares [Mon, 3 Jun 2024 18:13:40 +0000 (19:13 +0100)]
JAL-4421 Also add DMG filename to python script. Necessitates DS_Store for x64 and aarch64 versions, with changes in build.gradle and install4j10_template.install4j. Ensure all x64 references are x64 and not the (more correct) x86 -- java uses x64.
Ben Soares [Fri, 31 May 2024 23:45:58 +0000 (00:45 +0100)]
JAL-4421 Add DS_Store customisation to gradle. Add backgroundImage alias dump to --dump
Ben Soares [Fri, 31 May 2024 17:48:47 +0000 (18:48 +0100)]
JAL-4421 Python script for customising DS_Store. Separate out more names for DMG volumes in install4j and gradle. Channel specific icon positioning for channel specific DMG background images.
Ben Soares [Wed, 29 May 2024 15:25:34 +0000 (16:25 +0100)]
JAL-4409 Allow more URI schemes (e.g. file) to be opened in Jalview
Ben Soares [Wed, 29 May 2024 15:11:38 +0000 (16:11 +0100)]
JAL-4409 Allow more URI schemes (e.g. file) to filter through to Jalview
Ben Soares [Wed, 29 May 2024 12:08:09 +0000 (13:08 +0100)]
JAL-4414 Add SocketTimeoutException to exceptions that trigger File Not Found rather than Format Not Recognised
Ben Soares [Wed, 29 May 2024 11:58:57 +0000 (12:58 +0100)]
JAL-3196 Need more memory for the install4j process run by gradle
Ben Soares [Tue, 28 May 2024 21:14:17 +0000 (22:14 +0100)]
JAL-4409 JAL-4160 Don't let getdown turn jalviewX:// URIs into absolute local file paths. Allow getdown CLI memory setting with double-dash --jvmmemX
Ben Soares [Tue, 28 May 2024 14:33:54 +0000 (15:33 +0100)]
JAL-4417 Use a specified props file for consistent output
Ben Soares [Tue, 28 May 2024 13:40:03 +0000 (14:40 +0100)]
JAL-4409 TEMPORARY don't clean up image files from jalview.bin.CommandsTest.headlessOrGuiImageOutputTest failing on build server
Ben Soares [Tue, 28 May 2024 12:21:24 +0000 (13:21 +0100)]
JAL-4409 Ensure the specific scheme jalviewx is only for the release version
Ben Soares [Tue, 28 May 2024 12:03:31 +0000 (13:03 +0100)]
JAL-4409 Don't insist on HttpURLConnection, allows for file:/ protocol connection
Ben Soares [Mon, 27 May 2024 09:06:01 +0000 (10:06 +0100)]
Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown
Jim Procter [Fri, 24 May 2024 15:43:42 +0000 (16:43 +0100)]
JAL-4159 fix up test for applicable filters for pasimap
Jim Procter [Fri, 24 May 2024 15:36:37 +0000 (16:36 +0100)]
JAL-4159 fix PairwiseAlignmentPanelTest - reinstate correct recording of the endRes for each sequence aligned
Jim Procter [Fri, 24 May 2024 15:18:49 +0000 (16:18 +0100)]
JAL-4159 peek in a Jalview project's PCA viewer's title to decide if it is a "pasimap" viewer or some other Pcaviewer...
Jim Procter [Fri, 24 May 2024 14:25:07 +0000 (15:25 +0100)]
JAL-4257 JAL-4159 JAL-789 tidy up passing of score model to pairwise alignment directly/via pasimap and threading off the direct pairwise alignment calculation
James Procter [Sat, 16 Dec 2023 08:43:06 +0000 (08:43 +0000)]
JAL-789 pairwise alignment via calculations dialog, allowing score model to be changed
merged in with feature/JAL-4159_pasimap
James Procter [Fri, 15 Dec 2023 13:56:07 +0000 (13:56 +0000)]
JAL-4366 compute coverage on each side of the pairwise alignment
Jim Procter [Fri, 24 May 2024 11:32:48 +0000 (12:32 +0100)]
Merge branch 'jims/feature/JAL-4159_pasimap' into feature/JAL-4159_pasimap
Jim Procter [Fri, 24 May 2024 11:24:17 +0000 (12:24 +0100)]
Merge branch 'features/JAL-4257_adjustablegapparams_nw' into jims/feature/JAL-4159_pasimap
Jim Procter [Thu, 23 May 2024 17:18:39 +0000 (18:18 +0100)]
JAL-4159 fix sense of console/alignment output suppression flags and make sure all output is suppressed when computing pairwise alignments
Jim Procter [Thu, 23 May 2024 17:17:12 +0000 (18:17 +0100)]
JAL-4159 disable the score model combo box when pasimap is selected
MorellThomas [Thu, 23 May 2024 12:53:51 +0000 (14:53 +0200)]
mend
MorellThomas [Thu, 23 May 2024 12:50:03 +0000 (14:50 +0200)]
Fix PaSiMap taking scoreModels input and allow AlignSeq/PairwiseAlignPanel to take a ScoreMatrix
MorellThomas [Thu, 23 May 2024 08:19:42 +0000 (10:19 +0200)]
Fix PaSiMap not having the eigenvalues saved
MorellThomas [Wed, 22 May 2024 13:53:35 +0000 (15:53 +0200)]
revert build.gradle changes
MorellThomas [Wed, 22 May 2024 13:46:48 +0000 (15:46 +0200)]
Save PaSiMap with Jalview Session
MorellThomas [Wed, 22 May 2024 11:36:07 +0000 (13:36 +0200)]
Rectanuglar selection changed to Mouse Button 3 drag
Jim Procter [Tue, 21 May 2024 17:29:24 +0000 (18:29 +0100)]
JAL-4259 set title using original alignment window's title
Jim Procter [Tue, 21 May 2024 17:21:05 +0000 (18:21 +0100)]
JAL-4159 implement bounds for PASIMAP calculation - from 9 to 20000 sequences.
Jim Procter [Tue, 21 May 2024 17:18:20 +0000 (18:18 +0100)]
JAL-4159 connectivity should be computed for the sequences analysed with PAsiMap, not the alignment
Jim Procter [Tue, 21 May 2024 17:16:59 +0000 (18:16 +0100)]
JAL-4159 PASiMap currently doesn't support different score models
Jim Procter [Tue, 21 May 2024 17:15:11 +0000 (18:15 +0100)]
JAL-4159 sometimes the progress bar may not be available - null check
Ben Soares [Tue, 21 May 2024 17:02:14 +0000 (18:02 +0100)]
JAL-1054 Change one more (unused) url.openStream to use the HttpUtils wrapper for completeness
Ben Soares [Tue, 21 May 2024 16:56:44 +0000 (17:56 +0100)]
JAL-1054 Change the rest of the url.openConnection() calls to use the HttpUtils.openConnection(url) wrapper
Ben Soares [Tue, 21 May 2024 15:31:00 +0000 (16:31 +0100)]
JAL-4409 Adjust usage of HttpUtils.equivalentJalviewURLString() and pass jalviewX:// URL files to Jalview without changing them as Jalview now deals with them
Ben Soares [Tue, 21 May 2024 14:55:57 +0000 (15:55 +0100)]
JAL-4409 Make HttpUtils.equivalentJalviewUrlString 'non-destructive'
Jim Procter [Tue, 21 May 2024 14:46:05 +0000 (15:46 +0100)]
Merge branch 'feature/JAL-4159_pasimap' into spike/JAL-4159_pasimap_2113_series
loop in new progress bar and resolve formatting conflicts in PairwiseAlignPanel
Jim Procter [Tue, 21 May 2024 14:19:13 +0000 (15:19 +0100)]
JAL-4356 release date for 2.11.3.3 is 22nd May 2025
Jim Procter [Tue, 21 May 2024 14:19:13 +0000 (15:19 +0100)]
JAL-4356 release date for 2.11.3.3 is 22nd May 2025
Ben Soares [Mon, 20 May 2024 20:19:21 +0000 (21:19 +0100)]
JAL-4409 Also interpret jalviewX:// URIs in Jalview itself (for executable jar or command line start)
Ben Soares [Mon, 20 May 2024 20:11:02 +0000 (21:11 +0100)]
JAL-4397 Another fix on linux
Ben Soares [Fri, 17 May 2024 16:26:30 +0000 (17:26 +0100)]
JAL-4420 Add some debugging statements
Ben Soares [Fri, 17 May 2024 14:56:11 +0000 (15:56 +0100)]
JAL-4420 Tests for new FileUtils methods
Ben Soares [Fri, 17 May 2024 14:55:52 +0000 (15:55 +0100)]
JAL-4420 Allow preprocessing of arguments if they are all simply filenames (or URLs). Preprocessing involves adding --open arguments, and spotting and regrouping associated files such as annotations, features and tree files. These get --annotations argument etc. Add FileUtils tools to get basepath and extension of filename or URL whilst only in String form.
Ben Soares [Fri, 17 May 2024 14:11:48 +0000 (15:11 +0100)]
JAL-4409 Checking getdown jars up to date