Ben Soares [Tue, 18 Aug 2020 23:38:12 +0000 (00:38 +0100)]
JAL-3718 Added digestonly key to getdown.txt to copy file to alt or release when building, and to be included in the getdown digest. This key is completely ignored by the getdown-launcher. Looks in j8/j11digestonly.
gmungoc [Tue, 18 Aug 2020 13:59:12 +0000 (14:59 +0100)]
JAL-3692 parse multiline CDS location correctly
Ben Soares [Tue, 18 Aug 2020 07:40:33 +0000 (08:40 +0100)]
JAL-3676 Start of documentation in help pages logging.html
Jim Procter [Mon, 17 Aug 2020 15:56:52 +0000 (16:56 +0100)]
JAL-3675 release notes for JAL-3691
Jim Procter [Mon, 17 Aug 2020 15:53:31 +0000 (16:53 +0100)]
Merge branch 'patch/JAL-3691_No_score_models_available' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 17 Aug 2020 15:49:16 +0000 (16:49 +0100)]
JAL-3675 JAL-3561 documented in release notes
Jim Procter [Mon, 17 Aug 2020 15:38:49 +0000 (16:38 +0100)]
JAL-3675 report JAL-3702 as known defect
Jim Procter [Mon, 17 Aug 2020 15:25:07 +0000 (16:25 +0100)]
Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI' into releases/Release_2_11_1_Branch
Jim Procter [Mon, 17 Aug 2020 15:09:26 +0000 (16:09 +0100)]
JAL-3712 fix typos for rebuilding/updating getdown jars and added mention of mvn_cmd in the getdown building help.
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 14:10:35 +0000 (15:10 +0100)]
JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations
Jim Procter [Mon, 10 Aug 2020 14:02:53 +0000 (15:02 +0100)]
Merge branch 'releases/Release_2_11_1_Branch' into patch/JAL-3691_No_score_models_available
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
Ben Soares [Wed, 5 Aug 2020 21:57:13 +0000 (22:57 +0100)]
JAL-3691 Changed .toUppoerCase().startsWith(...) to .regionMatches(true,...) as upper-cased 'i' in Turkish is not 'I'.
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
git://source.jalview.org / jalview.git / log