Jim Procter [Wed, 5 Aug 2020 14:47:31 +0000 (15:47 +0100)]
Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Ben Soares [Tue, 4 Aug 2020 18:30:47 +0000 (19:30 +0100)]
JAL-3477 Improved command line arguments description in memory.html
Ben Soares [Tue, 4 Aug 2020 17:13:02 +0000 (18:13 +0100)]
JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html
Ben Soares [Mon, 3 Aug 2020 10:20:05 +0000 (11:20 +0100)]
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax
Jim Procter [Mon, 3 Aug 2020 13:38:19 +0000 (14:38 +0100)]
JAL-3675 report JAL-3701 as known defect
Jim Procter [Mon, 3 Aug 2020 13:10:41 +0000 (14:10 +0100)]
JAL-3675 release notes for JAL-3692
Jim Procter [Mon, 3 Aug 2020 12:45:49 +0000 (13:45 +0100)]
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 3 Aug 2020 11:06:42 +0000 (12:06 +0100)]
JAL-3692 fix up test for 2.11.1 series datamodel API
gmungoc [Mon, 27 Jul 2020 15:34:04 +0000 (16:34 +0100)]
JAL-3692 set CDS /product as EMBLCDSPROTEIN description
gmungoc [Mon, 27 Jul 2020 15:26:08 +0000 (16:26 +0100)]
JAL-3692 refactor/complete parsing, more unit test coverage
gmungoc [Fri, 24 Jul 2020 08:38:45 +0000 (09:38 +0100)]
JAL-3692 parse DE for description, and other refactoring...
gmungoc [Thu, 23 Jul 2020 10:43:32 +0000 (11:43 +0100)]
JAL-3692 URL tests updated
gmungoc [Wed, 22 Jul 2020 09:55:43 +0000 (10:55 +0100)]
JAL-3692 unit test (J03321), fixes, dbrefs; todo: protein mappings
gmungoc [Tue, 21 Jul 2020 11:22:18 +0000 (12:22 +0100)]
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)
Conflicts:
src/jalview/ws/dbsources/EmblXmlSource.java
src/jalview/ws/ebi/EBIFetchClient.java
Jim Procter [Wed, 29 Jul 2020 17:48:52 +0000 (18:48 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Jim Procter [Wed, 29 Jul 2020 17:47:40 +0000 (18:47 +0100)]
JAL-3371 JAL-2983 don't modify 'extent' of slider - this is managed by look and feel
Jim Procter [Wed, 29 Jul 2020 16:46:33 +0000 (17:46 +0100)]
JAL-3675 mention -open argument in the command line arguments table
Jim Procter [Wed, 29 Jul 2020 16:46:17 +0000 (17:46 +0100)]
JAL-3675 JAL-3570 JAL-3608 JAL-2983 release notes and docs
Jim Procter [Tue, 28 Jul 2020 12:43:48 +0000 (13:43 +0100)]
JAL-3675 update release note for JAL-2656
Jim Procter [Tue, 28 Jul 2020 10:32:46 +0000 (11:32 +0100)]
JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header
Jim Procter [Tue, 28 Jul 2020 10:29:20 +0000 (11:29 +0100)]
JAL-2656 recognise Gzipped file input streams by their content, not their filename
Jim Procter [Tue, 28 Jul 2020 10:18:56 +0000 (11:18 +0100)]
JAL-3615 update tests for Rfam/Pfam specific gzip endpoints
Jim Procter [Mon, 27 Jul 2020 18:15:16 +0000 (19:15 +0100)]
JAL-3675 release notes for JAL-3615 and JAL-2656
gmungoc [Thu, 2 Jul 2020 16:24:28 +0000 (17:24 +0100)]
JAL-2656 JAL-3615 check response headers to test for gzipped url reply
gmungoc [Thu, 2 Jul 2020 14:28:36 +0000 (15:28 +0100)]
JAL-3615 used gzip endpoints for Pfam and Rfam
redact parent commits related to JalviewJS for 2.11.1.1 patch
Jim Procter [Mon, 27 Jul 2020 15:46:47 +0000 (16:46 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Conflict in way transparency slider was inited - followed HEAD's pattern here.
Jim Procter [Mon, 27 Jul 2020 15:16:34 +0000 (16:16 +0100)]
JAL-3675 release notes for JAL-3621
gmungoc [Tue, 19 May 2020 17:27:40 +0000 (18:27 +0100)]
JAL-3621 corrected sequence feature sort and test
gmungoc [Mon, 18 May 2020 14:57:13 +0000 (15:57 +0100)]
JAL-3621 update to intervalstore v1.1
Jim Procter [Mon, 27 Jul 2020 14:50:50 +0000 (15:50 +0100)]
JAL-3675 release notes for JAL-3695 JAL-3696 JAL-3697
Jim Procter [Mon, 27 Jul 2020 14:10:11 +0000 (15:10 +0100)]
JAL-3697 show total number of features not shown
Jim Procter [Mon, 27 Jul 2020 14:05:30 +0000 (15:05 +0100)]
JAL-3696 log the error message from the exception to the console
Jim Procter [Mon, 27 Jul 2020 13:59:51 +0000 (14:59 +0100)]
JAL-3695 htsjdk 2.12 -> 2.23 (library change only, no code change. needs gradle refresh in eclipse)
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
git://source.jalview.org / jalview.git / log