Jim Procter [Mon, 17 Aug 2020 11:13:03 +0000 (12:13 +0100)]
JAL-3490 JAL-3675 release notes, update Find dialog image in help and tidy up documentation for 2.11.1.1
Jim Procter [Mon, 17 Aug 2020 10:03:57 +0000 (11:03 +0100)]
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 17 Aug 2020 09:51:05 +0000 (10:51 +0100)]
JAL-3675 JAL-3597 release notes
Jim Procter [Mon, 17 Aug 2020 09:03:47 +0000 (10:03 +0100)]
Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch' into releases/Release_2_11_1_Branch
Ben Soares [Fri, 14 Aug 2020 12:01:06 +0000 (13:01 +0100)]
JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.
Ben Soares [Thu, 13 Aug 2020 22:05:00 +0000 (23:05 +0100)]
JAL-3597 Increased heap passmark to <= 45MB and report smallest of failed attempts heap size
gmungoc [Mon, 20 Jul 2020 08:17:29 +0000 (09:17 +0100)]
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB
gmungoc [Tue, 14 Jul 2020 08:43:50 +0000 (09:43 +0100)]
JAL-3597 additional references nulled, bug in test corrected
Jim Procter [Thu, 13 Aug 2020 16:51:44 +0000 (17:51 +0100)]
JAL-3675 brought forward patch to build.gradle for changed main class variable in build.properties
Jim Procter [Thu, 13 Aug 2020 14:53:53 +0000 (15:53 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' of source.jalview.org/git/jalview into releases/Release_2_11_1_Branch
Ben Soares [Wed, 12 Aug 2020 12:48:57 +0000 (13:48 +0100)]
JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.
Jim Procter [Wed, 12 Aug 2020 12:29:23 +0000 (13:29 +0100)]
JAL-3675 added JAL-3576 as known defect (colocated features appear in different order when exported/reimported)
Ben Soares [Tue, 7 Jul 2020 23:47:55 +0000 (00:47 +0100)]
JAL-3608 Changes from code review CR-JAL-236
Conflicts:
src/jalview/bin/Jalview.java
Jim Procter [Tue, 11 Aug 2020 15:24:26 +0000 (16:24 +0100)]
JAL-3675 fix issue attribution for JAL-3667 release note line
Jim Procter [Tue, 11 Aug 2020 14:54:24 +0000 (15:54 +0100)]
JAL-3675 update release notes for JAL-3673 and tested merge of additional patch for JAL-2983
Jim Procter [Fri, 26 Jun 2020 16:24:16 +0000 (17:24 +0100)]
JAL-3673 make sure font metrics are updated if dealing with reference sequence font !
Jim Procter [Tue, 11 Aug 2020 14:01:10 +0000 (15:01 +0100)]
Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
gmungoc [Tue, 11 Aug 2020 09:35:32 +0000 (10:35 +0100)]
JAL-3371 more fine-grained slider; set Param slider to initial default
gmungoc [Thu, 6 Aug 2020 08:49:23 +0000 (09:49 +0100)]
JAL-3490 match count independent of contiguous matches count
Jim Procter [Mon, 10 Aug 2020 14:01:23 +0000 (15:01 +0100)]
JAL-3628 JAL-3708 call Cache.initLogger() before using Cache.log in static methods with no class-level guarantee logs are initialised
Jim Procter [Wed, 5 Aug 2020 16:41:36 +0000 (17:41 +0100)]
JAL-3628 init log after loading testProps for each backupfile test
Jim Procter [Wed, 5 Aug 2020 16:29:19 +0000 (17:29 +0100)]
Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch
gmungoc [Wed, 5 Aug 2020 16:01:37 +0000 (17:01 +0100)]
JAL-3692 unit test updated for ?gzip download endpoint URL
gmungoc [Wed, 5 Aug 2020 15:53:17 +0000 (16:53 +0100)]
JAL-3692 parse multiline feature qualifiers and escaped quotes
Jim Procter [Wed, 5 Aug 2020 15:41:48 +0000 (16:41 +0100)]
JAL-3675 release notes for JAL-3477, JAL-3667, JAL-3541, JAL-3685, JAL-3676, JAL-3677 and bumped release date for 2.11.1.1 to next Tuesday(ish)
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
git://source.jalview.org / jalview.git / log