Ben Soares [Thu, 30 Jul 2020 11:05:49 +0000 (12:05 +0100)]
JAL-3633 Help documentation updated
Ben Soares [Wed, 29 Jul 2020 18:48:02 +0000 (19:48 +0100)]
JAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview-JS, Most NPE fixes for tests
Ben Soares [Wed, 29 Jul 2020 11:44:24 +0000 (12:44 +0100)]
JAL-3275 JAL-3633: JAL-3275 Turned Preferences into a Singleton that checks renews if it's been closed. Removed some debugging for JAL-3633. Added focus/highlight to proxy password box when needed. Forced WS lookup wheb proxy settings changed.
Ben Soares [Mon, 27 Jul 2020 19:31:16 +0000 (20:31 +0100)]
JAL-3633 Set proxy preferences before web calls in jalview.bin.Jalview. Fixed call to open Preferences->Connections with message when required.
Ben Soares [Sat, 25 Jul 2020 23:41:42 +0000 (00:41 +0100)]
JAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab when proxy password needed
Ben Soares [Wed, 22 Jul 2020 18:40:59 +0000 (19:40 +0100)]
JAL-3633 Added Proxy Authentication credentials in Preferences and set via java.net.Authenticator
Ben Soares [Tue, 21 Jul 2020 19:47:18 +0000 (20:47 +0100)]
JAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet
Ben Soares [Tue, 21 Jul 2020 11:41:31 +0000 (12:41 +0100)]
JAL-3633 label.proxy_server -> label.proxy_servers
Ben Soares [Sun, 12 Jul 2020 23:31:13 +0000 (00:31 +0100)]
JAL-3633 Remember system set proxy properties. Add options in Preferences for No proxy, system proxy, or custom proxy servers.
Ben Soares [Fri, 10 Jul 2020 00:03:18 +0000 (01:03 +0100)]
JAL-3609 JAL-3633 merged getdown jars
Ben Soares [Fri, 10 Jul 2020 00:01:11 +0000 (01:01 +0100)]
Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch
Ben Soares [Thu, 9 Jul 2020 14:57:48 +0000 (15:57 +0100)]
JAL-3633 Compiled jars for pass getdown proxy settings in proxy.txt on to Jalview
Ben Soares [Thu, 9 Jul 2020 14:57:19 +0000 (15:57 +0100)]
JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview
Ben Soares [Wed, 8 Jul 2020 16:01:32 +0000 (17:01 +0100)]
JAL-3633 ensure check both or https:// for urls
Ben Soares [Wed, 8 Jul 2020 14:45:54 +0000 (15:45 +0100)]
Merge branch 'bug/JAL-3541_cherry_pick_to_releases_Release_2_11_1_Branch' into task/JAL-3608_and_JAL-3609_merged_for_Release_2_11_1_Branch
Ben Soares [Wed, 8 Jul 2020 13:37:24 +0000 (14:37 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into task/JAL-3608_and_JAL-3609_merged_for_Release_2_11_1_Branch
Ben Soares [Wed, 8 Jul 2020 11:25:26 +0000 (12:25 +0100)]
Merge branch 'task/JAL-3609_HiDPI_support_in_java' into task/JAL-3608_and_JAL-3609_merged_for_Release_2_11_1_Branch
Ben Soares [Tue, 7 Jul 2020 23:02:18 +0000 (00:02 +0100)]
JAL-3608 Changes from code review CR-JAL-236
Ben Soares [Tue, 7 Jul 2020 19:58:03 +0000 (20:58 +0100)]
JAL-3608 ex stacktraces now go to Cache.log.debug
Ben Soares [Tue, 7 Jul 2020 19:42:23 +0000 (20:42 +0100)]
JAL-3628 System.out/err -> Cache.log.info/error
Ben Soares [Tue, 7 Jul 2020 19:39:04 +0000 (20:39 +0100)]
Merge branch 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' into task/JAL-3608_property_set_laf_and_tests_from_Release_2_11_1_Branch
Ben Soares [Tue, 7 Jul 2020 19:35:39 +0000 (20:35 +0100)]
JAL-3628 System.out/err -> Cache.log.info/error
Ben Soares [Wed, 27 May 2020 16:37:12 +0000 (17:37 +0100)]
JAL-3541 ensure deletion of cloverReportDir
Ben Soares [Wed, 27 May 2020 15:53:40 +0000 (16:53 +0100)]
JAL-3541 small fix for clover.xml location expected by build server plugin, and comment clarity
soares [Tue, 26 May 2020 14:08:17 +0000 (15:08 +0100)]
JAL-3541 added a property/variable style comment to build.gradle
Ben Soares [Fri, 15 May 2020 00:03:57 +0000 (01:03 +0100)]
JAL-3541 Fixed report path for build artifacts
Ben Soares [Thu, 14 May 2020 20:11:47 +0000 (21:11 +0100)]
JAL-3541 Added mem setting and jvmArgs for cloverReporting
Ben Soares [Thu, 14 May 2020 14:53:00 +0000 (15:53 +0100)]
JAL-3541 Individual tests now instrumented and reported. Added cloverConsoleReport.
Ben Soares [Tue, 12 May 2020 22:05:58 +0000 (23:05 +0100)]
JAL-3541 Helpers for running tests, and other commands headlessly
Ben Soares [Tue, 12 May 2020 22:05:14 +0000 (23:05 +0100)]
JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.
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
Ben Soares [Wed, 18 Mar 2020 11:33:26 +0000 (11:33 +0000)]
JAL-3541 perhaps a better clean for clover. fixed
Ben Soares [Wed, 18 Mar 2020 11:21:37 +0000 (11:21 +0000)]
JAL-3541 perhaps a better clean for clover
Ben Soares [Tue, 17 Mar 2020 19:19:59 +0000 (19:19 +0000)]
JAL-3541 rejigged clover tasks very mildly
Ben Soares [Tue, 7 Jul 2020 00:50:05 +0000 (01:50 +0100)]
JAL-3685 Fixed single quotes in formatMessage messages
Ben Soares [Tue, 7 Jul 2020 00:30:23 +0000 (01:30 +0100)]
JAL-3628 Fixed oddly worded and non-formatted error popups when saving fails
Ben Soares [Mon, 6 Jul 2020 15:42:40 +0000 (16:42 +0100)]
Merge branch 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' of https://source.jalview.org/git/jalview into bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows
Ben Soares [Mon, 6 Jul 2020 15:40:25 +0000 (16:40 +0100)]
Merge branch 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' of https://source.jalview.org/git/jalview into bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows
Ben Soares [Mon, 6 Jul 2020 14:54:52 +0000 (15:54 +0100)]
JAL-3676 improvement for visual selection of console text - fg color change if required
Ben Soares [Mon, 6 Jul 2020 15:27:36 +0000 (16:27 +0100)]
Merge branch 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' of https://source.jalview.org/git/jalview into bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows
Ben Soares [Mon, 6 Jul 2020 14:54:52 +0000 (15:54 +0100)]
JAL-3628 improvement for visual selection of console text - fg color change if required
Ben Soares [Mon, 6 Jul 2020 14:43:37 +0000 (15:43 +0100)]
JAL-3628 Fix for slightly incorrect boolean usage to determine success when rolling backup files
Ben Soares [Mon, 6 Jul 2020 13:48:59 +0000 (14:48 +0100)]
JAL-3628 Even more Cache.log.debug statements
gmungoc [Mon, 6 Jul 2020 11:37:41 +0000 (12:37 +0100)]
JAL-3570 JAL-3187 spanish translations for tabbed feature settings
gmungoc [Mon, 6 Jul 2020 09:05:25 +0000 (10:05 +0100)]
JAL-3570 updated external help links
Jim Procter [Sat, 4 Jul 2020 14:11:45 +0000 (15:11 +0100)]
Merge branch 'merge/JAL-3609_and_JAL-3608' into releases/Release_2_11_1_Branch
Jim Procter [Sat, 4 Jul 2020 13:37:41 +0000 (14:37 +0100)]
JAL-3675 version update and documentation for JAL-3493 JAL-3680 JAL-3638
Jim Procter [Sat, 4 Jul 2020 12:47:17 +0000 (13:47 +0100)]
JAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in cursor mode.
Jim Procter [Sat, 4 Jul 2020 12:45:52 +0000 (13:45 +0100)]
JAL-3638 don’t move cursor to next gap after moving selection up and down with shift+Alt+up/down
Jim Procter [Sat, 4 Jul 2020 12:17:00 +0000 (13:17 +0100)]
JAL-3680 check whether a sequence selection exists before sliding the sequence under the cursor when sliding sequences
Jim Procter [Tue, 2 Jun 2020 17:03:32 +0000 (18:03 +0100)]
JAL-3638 shift+arrow keys in cursor mode jumps cursor in a gapped region to next aligned position, and when at an aligned position jumps to next gapped region
Ben Soares [Sat, 4 Jul 2020 12:17:42 +0000 (13:17 +0100)]
JAL-3628 More Cache.log.debug statements
Ben Soares [Thu, 2 Jul 2020 14:36:41 +0000 (15:36 +0100)]
JAL-3676 code review -- added non-listed Level into dropdown list
Ben Soares [Wed, 1 Jul 2020 14:37:35 +0000 (15:37 +0100)]
JAL-3609 Allow pass-through of setHiDPIScale property to tests via (e.g.) gradle test -Ptest_HiDPIScale=2
Ben Soares [Wed, 1 Jul 2020 13:55:55 +0000 (14:55 +0100)]
Merge branch 'task/JAL-3608_property_set_laf_and_tests_from_Release_2_11_1_Branch' into merge/JAL-3609_and_JAL-3608
Ben Soares [Tue, 30 Jun 2020 15:04:00 +0000 (16:04 +0100)]
JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console
Jim Procter [Mon, 29 Jun 2020 16:46:57 +0000 (17:46 +0100)]
JAL-3675 2.11.1.1 release notes
Jim Procter [Mon, 29 Jun 2020 16:27:20 +0000 (17:27 +0100)]
Merge branch 'patch/Clear_Highlight_JAL-3493' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 29 Jun 2020 16:24:29 +0000 (17:24 +0100)]
JAL-3493 clear search highlights when escape/deselect all
Jim Procter [Mon, 29 Jun 2020 16:19:19 +0000 (17:19 +0100)]
JAL-3493 failing test - creates a highlight and column selection and then called the deselect all alignfjame action and checks if highlight and selection are still present.
Ben Soares [Wed, 24 Jun 2020 22:29:40 +0000 (23:29 +0100)]
JAL-3667 Fixed single backupfile error deleting the backupfile. Changed console output to Cache.log....
Ben Soares [Sun, 21 Jun 2020 00:24:10 +0000 (01:24 +0100)]
JAL-3609 Report when scale setting used.
Ben Soares [Sun, 21 Jun 2020 00:23:37 +0000 (01:23 +0100)]
JAL-3609 New auto-scale 'formula' for linux HiDPI. Tested to work for UHD screen in various OS display settings.
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
Ben Soares [Mon, 15 Jun 2020 19:22:29 +0000 (20:22 +0100)]
JAL-3628 Changed other calls to renameTo to use BackupFiles.moveFileToFile
Ben Soares [Mon, 8 Jun 2020 23:49:34 +0000 (00:49 +0100)]
JAL-3628 Changed all file1.renameTo(file2) calls to Files.move(path1,path2,REPLACE_EXISTING) in jalview.io.BackupFiles. This fixes a problem in Windows with renameTo when destination file already exists.
soares [Fri, 22 May 2020 11:56:04 +0000 (12:56 +0100)]
JAL-3609 corrected maxdimension to mindimension. Adjusted tallscreen limit
Ben Soares [Wed, 20 May 2020 17:25:34 +0000 (18:25 +0100)]
JAL-3609 removed debugging prints
Ben Soares [Tue, 19 May 2020 19:32:27 +0000 (20:32 +0100)]
JAL-3609 changed property names to something more palatable and catered for portrait screens
Ben Soares [Tue, 19 May 2020 17:15:01 +0000 (18:15 +0100)]
JAL-3609 system properties to force a scale, or automatically choose based on OS, Screen DPI and Screen height in pixels
Ben Soares [Tue, 19 May 2020 00:38:58 +0000 (01:38 +0100)]
JAL-3609 Added a -DforceHiDPISetting=true option mainly for testing, and updated getdown HiDPISetting
gmungoc [Mon, 18 May 2020 08:39:55 +0000 (09:39 +0100)]
JAL-3613 remove debug code committed in error
Ben Soares [Fri, 15 May 2020 20:04:39 +0000 (21:04 +0100)]
JAL-3609 HiDPI scale setting done via system prop in getdown or halview.bin.Launcher
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 [Wed, 22 Apr 2020 10:43:00 +0000 (11:43 +0100)]
Merge branch 'releases/Release_2_11_1_Branch'
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
git://source.jalview.org / jalview.git / log