Jim Procter [Tue, 16 Apr 2019 16:38:59 +0000 (17:38 +0100)]
JAL-3130 tidy up system.output
Jim Procter [Tue, 16 Apr 2019 16:38:18 +0000 (17:38 +0100)]
JAL-3130 call Jalview via the Test JVM’s JAVA_HOME/bin/java
Jim Procter [Tue, 16 Apr 2019 16:36:45 +0000 (17:36 +0100)]
JAL-3130 refactored ‘clover’ to ‘use_clover’ since clover is an ambiguous property - still offer -Pclover=true as command line switch to enable clover coverage
Jim Procter [Tue, 16 Apr 2019 15:06:52 +0000 (16:06 +0100)]
JAL-3130 JAL-1889 reportCurrentWorkingDirectory test to report absolute path when running command line tests
Jim Procter [Tue, 16 Apr 2019 13:28:44 +0000 (14:28 +0100)]
JAL-3130 JAL-1889 report absolute paths for CommandLineTests
Jim Procter [Tue, 16 Apr 2019 13:14:10 +0000 (14:14 +0100)]
JAL-3130 JAL-1889 report absolute paths for CommandLineTests
Jim Procter [Tue, 16 Apr 2019 13:09:12 +0000 (14:09 +0100)]
JAL-3130 JAL-1889 report absolute paths for CommandLineTests
Jim Procter [Tue, 16 Apr 2019 12:29:10 +0000 (13:29 +0100)]
JAL-3196 change default are resource properties to jalview.org/getdown/jre
Jim Procter [Tue, 16 Apr 2019 10:01:10 +0000 (11:01 +0100)]
Reinstate imports from "JAL-1889 JAL-3130 patch broken tests" commit
05efc2ac3c6427a4dabce842ebbd6f2ae17f49b9.
Jim Procter [Tue, 16 Apr 2019 09:33:42 +0000 (10:33 +0100)]
JAL-1189 JAL-3130 patch broken tests
Ben Soares [Mon, 15 Apr 2019 16:26:30 +0000 (17:26 +0100)]
JAL-3130 Somewhere in the old libs the Jws2 client is working. Compile with Java 11 in Java 1.8 target mode, and then run in Java1.8 JRE with 'java -cp "j8lib/*:classes" jalview.bin.Jalview'. Will need to find out which of these is actually needed
Ben Soares [Mon, 15 Apr 2019 16:24:38 +0000 (17:24 +0100)]
JAL-3130 Helper classes to take Class Exceptions when run in java 1.8 JRE out of main classes
Ben Soares [Mon, 15 Apr 2019 16:17:09 +0000 (17:17 +0100)]
JAL-3130 some clover fixes for helplinks. Use 'gradle test -Pclover=true'
Ben Soares [Mon, 15 Apr 2019 09:25:36 +0000 (10:25 +0100)]
JAL-3130 adapted getdown src. attempt 2. first attempt failed due to cp'ed .git files
Jim Procter [Sun, 14 Apr 2019 20:22:45 +0000 (21:22 +0100)]
JAL-3130 write clover.xml during cloverReport phase
Jim Procter [Sun, 14 Apr 2019 10:48:05 +0000 (11:48 +0100)]
JAL-3130 make sure testng-results.xml is generated
Jim Procter [Fri, 12 Apr 2019 16:36:22 +0000 (17:36 +0100)]
JAL-3130 specify module list when launching new Jalview for CLI tests
Jim Procter [Fri, 12 Apr 2019 16:35:32 +0000 (17:35 +0100)]
JAL-3130 instrument main and compile separately to test classes so Clover doesn’t misclassify them
Jim Procter [Fri, 12 Apr 2019 15:06:54 +0000 (16:06 +0100)]
JAL-3130 gradle test now runs open clover 4.3.1 and new cloverReport task
Jim Procter [Thu, 11 Apr 2019 13:52:20 +0000 (14:52 +0100)]
Merge branch 'develop' into task/JAL-3130_Java_11_investigations-getdown_src
Jim Procter [Thu, 11 Apr 2019 13:37:58 +0000 (14:37 +0100)]
JAL-3130 ensure J11 libs/modules are added when building and running test suite
Jim Procter [Thu, 11 Apr 2019 13:37:08 +0000 (14:37 +0100)]
JAL-3130 clean up eclipse class path for dependencies moved to j11lib
gmungoc [Wed, 10 Apr 2019 20:35:10 +0000 (21:35 +0100)]
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
gmungoc [Wed, 10 Apr 2019 20:20:22 +0000 (21:20 +0100)]
JAL-3018 REST version updated to 10.0
Ben Soares [Fri, 5 Apr 2019 17:01:18 +0000 (18:01 +0100)]
JAL-3130 adapted getdown src
Ben Soares [Fri, 5 Apr 2019 16:19:07 +0000 (17:19 +0100)]
JAL-3130 This commit concentrates on the Mac OS X DMG app bundle, ensuring only one JRE needed in the .app bundle for 1) install4j, 2) getdown, 3) jalview
Ben Soares [Thu, 4 Apr 2019 10:10:01 +0000 (11:10 +0100)]
JAL-3130 trying to be Java 1.8 source compatible -- not sure if this is ultimately feasible in the same .java files
Ben Soares [Thu, 4 Apr 2019 10:09:04 +0000 (11:09 +0100)]
JAL-3130 JAL-3007 more files needed for getdown launcher
Ben Soares [Thu, 4 Apr 2019 10:08:07 +0000 (11:08 +0100)]
JAL-3130 JAL-3007 improvements to gradle build
gmungoc [Wed, 3 Apr 2019 15:43:19 +0000 (16:43 +0100)]
JAL-3021 show Sequence Details with cursor at top
Ben Soares [Mon, 1 Apr 2019 16:04:56 +0000 (17:04 +0100)]
JAL-3130 JAL-3007 Added gradle build for Java 11. Now in root jalview dir
Ben Soares [Mon, 1 Apr 2019 08:53:21 +0000 (09:53 +0100)]
JAL-3130 JAL-3007 Added gradle build for Java 11 and additional taskbar icon change in jalview.bin.Jalview
gmungoc [Fri, 29 Mar 2019 11:05:29 +0000 (11:05 +0000)]
JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar
gmungoc [Fri, 29 Mar 2019 10:31:02 +0000 (10:31 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 Mar 2019 10:30:51 +0000 (10:30 +0000)]
JAL-3140 intervalstore now v1.0 (public release)
Jim Procter [Fri, 29 Mar 2019 09:54:49 +0000 (09:54 +0000)]
JAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete
Jim Procter [Thu, 28 Mar 2019 17:34:20 +0000 (17:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Mar 2019 17:34:11 +0000 (17:34 +0000)]
JAL-3111 biojava dependencies
Jim Procter [Thu, 28 Mar 2019 17:20:31 +0000 (17:20 +0000)]
JAL-3111 fix libquagua dependency paths - needs to be checked on OSX InstallAnywhere
Jim Procter [Thu, 28 Mar 2019 17:20:04 +0000 (17:20 +0000)]
JAL-3111 fix jabaws dependency name in IA config
Jim Procter [Thu, 28 Mar 2019 16:59:51 +0000 (16:59 +0000)]
JAL-3111 intervalstore library on IA classpath
gmungoc [Thu, 28 Mar 2019 16:13:39 +0000 (16:13 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Thu, 28 Mar 2019 15:55:08 +0000 (15:55 +0000)]
JAL-3111 typo in IA config
gmungoc [Thu, 28 Mar 2019 15:52:34 +0000 (15:52 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 28 Mar 2019 15:52:23 +0000 (15:52 +0000)]
JAL-1889 patch for failing isControDown test on build server
Jim Procter [Thu, 28 Mar 2019 15:40:20 +0000 (15:40 +0000)]
JAL-3111 update InstallAnywhere dependencies for changed libraries
gmungoc [Thu, 28 Mar 2019 07:56:40 +0000 (07:56 +0000)]
Merge branch 'feature/JAL-3181linkOrdering' into develop
gmungoc [Wed, 27 Mar 2019 17:06:12 +0000 (17:06 +0000)]
JAL-2620 improved error reporting on failure to load resource files
gmungoc [Mon, 25 Mar 2019 16:21:42 +0000 (16:21 +0000)]
JAL-2717 adjusted code so default correctly returned if i18n fails
gmungoc [Mon, 25 Mar 2019 08:57:56 +0000 (08:57 +0000)]
JAL-3127 scripts updated for method signature change
gmungoc [Sat, 23 Mar 2019 08:49:52 +0000 (08:49 +0000)]
JAL-1889 explicit recalc of geometry for scale left/right/above on/off
gmungoc [Sat, 23 Mar 2019 06:40:38 +0000 (06:40 +0000)]
JAL-1889 remove debug logging, add updateLayout()
Ben Soares [Fri, 22 Mar 2019 16:23:33 +0000 (16:23 +0000)]
JAL-3130 adding two more modules picked up by gradle building -- not sure why these hadn't been missed before by ant
Ben Soares [Fri, 22 Mar 2019 16:22:45 +0000 (16:22 +0000)]
JAL-3130 mark some deprecated methods in Regex as @Deprecated to stop warnings
gmungoc [Fri, 22 Mar 2019 14:38:08 +0000 (14:38 +0000)]
JAL-1889 more debug logging
gmungoc [Thu, 21 Mar 2019 16:28:40 +0000 (16:28 +0000)]
JAL-1889 better debug logging
gmungoc [Thu, 21 Mar 2019 15:59:39 +0000 (15:59 +0000)]
JAL-1889 temporary debug in findColumn()
gmungoc [Thu, 21 Mar 2019 15:44:48 +0000 (15:44 +0000)]
JAL-1889 added belt and braces deleteOnExit() to test output file
gmungoc [Thu, 21 Mar 2019 15:33:51 +0000 (15:33 +0000)]
JAL-1889 correct props param, remove dasserver, output file paths
Ben Soares [Thu, 21 Mar 2019 15:31:15 +0000 (15:31 +0000)]
JAL-3130 Replaced deprecated Class.newInstance() with Class.getDeclaredConstructor().newInstance(). Some eclipse fixes have appeared too.
gmungoc [Thu, 21 Mar 2019 13:26:14 +0000 (13:26 +0000)]
JAL-1889 more diagnostics for CommandLineOperations
gmungoc [Thu, 21 Mar 2019 10:12:06 +0000 (10:12 +0000)]
JAL-1889 diagnostics for failing test on server
Ben Soares [Wed, 20 Mar 2019 16:13:14 +0000 (16:13 +0000)]
JAL-3130 Lots of deprecation fixes. See utils/deprecation_auto_fixes.sh for commands used to fix the bulk of these (a couple of manual fixes at the end too).
gmungoc [Wed, 20 Mar 2019 14:35:34 +0000 (14:35 +0000)]
JAL-3093 fine tuning of SeqPanel tooltip
gmungoc [Wed, 20 Mar 2019 12:25:31 +0000 (12:25 +0000)]
JAL-3212 unit test and fix for Scale Panel bug
Ben Soares [Tue, 19 Mar 2019 16:02:11 +0000 (16:02 +0000)]
JAL-3130 remove some comments on quit. fix modules file.
Ben Soares [Tue, 19 Mar 2019 14:58:52 +0000 (14:58 +0000)]
JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben-2 and updated develop
Ben Soares [Mon, 18 Mar 2019 16:53:02 +0000 (16:53 +0000)]
JAL-3130 removing no longer needed JRE (going to use adoptopenjdk jre11)
Ben Soares [Mon, 18 Mar 2019 16:50:09 +0000 (16:50 +0000)]
JAL-3130 Removing accidentally committed tmp dir
gmungoc [Fri, 15 Mar 2019 14:57:54 +0000 (14:57 +0000)]
JAL-2964 missed branch for restore link tree to all views
gmungoc [Fri, 15 Mar 2019 14:17:44 +0000 (14:17 +0000)]
JAL-3203 Overview show hidden default false also in Preferences
gmungoc [Tue, 12 Mar 2019 09:04:21 +0000 (09:04 +0000)]
JAL-1270 missing 'alwaysRun=true' added to setup/teardown
gmungoc [Tue, 12 Mar 2019 08:18:42 +0000 (08:18 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
gmungoc [Tue, 12 Mar 2019 08:18:07 +0000 (08:18 +0000)]
JAL-3127 check for null viewport
gmungoc [Mon, 11 Mar 2019 16:32:45 +0000 (16:32 +0000)]
Merge branch 'develop' into merge/JAL-3127
gmungoc [Mon, 11 Mar 2019 16:30:12 +0000 (16:30 +0000)]
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test AfterMethod!
gmungoc [Mon, 11 Mar 2019 15:36:36 +0000 (15:36 +0000)]
JAL-3127 fix faulty merge
gmungoc [Mon, 11 Mar 2019 15:07:39 +0000 (15:07 +0000)]
Merge branch 'develop' into merge/JAL-3127
Conflicts:
src/jalview/viewmodel/AlignmentViewport.java
gmungoc [Mon, 11 Mar 2019 15:04:23 +0000 (15:04 +0000)]
Merge branch 'feature/JAL-2250colourAllGroups' into develop
gmungoc [Mon, 11 Mar 2019 14:54:26 +0000 (14:54 +0000)]
JAL-3201 restore group colours correctly from project
gmungoc [Mon, 11 Mar 2019 11:37:58 +0000 (11:37 +0000)]
Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127
Conflicts:
src/jalview/gui/Jalview2XML.java
src/jalview/gui/Jalview2XML_V1.java
test/jalview/io/Jalview2xmlTests.java
gmungoc [Mon, 11 Mar 2019 08:50:41 +0000 (08:50 +0000)]
JAL-3206 strict above/below threshold test restored
gmungoc [Mon, 11 Mar 2019 08:45:18 +0000 (08:45 +0000)]
Merge branch 'bug/JAL-3075' into develop
gmungoc [Fri, 8 Mar 2019 14:37:26 +0000 (14:37 +0000)]
JAL-3193 defensive trim of URL read from properties file
gmungoc [Fri, 8 Mar 2019 11:55:15 +0000 (11:55 +0000)]
JAL-2903 typos fixed
gmungoc [Fri, 8 Mar 2019 11:26:52 +0000 (11:26 +0000)]
JAL-3075 update column selection on mouse up after scroll
gmungoc [Thu, 7 Mar 2019 16:12:25 +0000 (16:12 +0000)]
Merge branch 'feature/JAL-3180colourAnnotationMenu' into merge/JAL-3180
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
Ben Soares [Thu, 7 Mar 2019 15:29:38 +0000 (15:29 +0000)]
JAL-3130 deprecation change preparation
gmungoc [Thu, 7 Mar 2019 15:08:15 +0000 (15:08 +0000)]
JAL-2250 default Apply Colour to All Groups selected
Jim Procter [Thu, 7 Mar 2019 14:25:41 +0000 (14:25 +0000)]
JAL-3127 set ‘updateStructures’ flag for viewports associated with each tree to true when groups are deleted, rather then when we create new groups (which may not always be the case).
gmungoc [Thu, 7 Mar 2019 12:57:28 +0000 (12:57 +0000)]
JAL-2717 JAL-2360 belated unit tests for ColourMenuHelper
gmungoc [Tue, 21 Aug 2018 12:59:37 +0000 (13:59 +0100)]
JAL-2717 corrected i18n of colour scheme names
gmungoc [Thu, 7 Mar 2019 09:14:33 +0000 (09:14 +0000)]
Merge branch 'feature/JAL-3205symmetricCalc' into develop
gmungoc [Thu, 7 Mar 2019 08:43:44 +0000 (08:43 +0000)]
JAL-3035 removed spring libraries as only used for jdas
gmungoc [Wed, 6 Mar 2019 16:01:34 +0000 (16:01 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 16:01:12 +0000 (16:01 +0000)]
JAL-3035 restored erroneous deletion
gmungoc [Wed, 6 Mar 2019 15:50:20 +0000 (15:50 +0000)]
Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop
gmungoc [Wed, 6 Mar 2019 15:49:46 +0000 (15:49 +0000)]
JAL-3035 more das bits removed
gmungoc [Tue, 5 Mar 2019 17:57:54 +0000 (17:57 +0000)]
Merge branch 'bug/JAL-3201groupClustal' into develop
gmungoc [Tue, 5 Mar 2019 16:44:20 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/features/JAL-2620alternativeCodeTables' into merge/JAL-2620
git://source.jalview.org / jalview.git / log