gmungoc [Mon, 8 Jun 2020 15:17:55 +0000 (16:17 +0100)]
JAL-3390 obsolete classes/methods removed
gmungoc [Mon, 8 Jun 2020 15:14:08 +0000 (16:14 +0100)]
Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure
Conflicts:
gradle.properties
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/api/structures/JalviewStructureDisplayI.java
src/jalview/appletgui/AppletJmol.java
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/ext/rbvi/chimera/AtomSpecModel.java
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/AlignmentPanel.java
src/jalview/gui/AppJmol.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/JalviewChimeraBindingModel.java
src/jalview/gui/StructureViewerBase.java
src/jalview/structures/models/AAStructureBindingModel.java
test/jalview/ext/jmol/JmolCommandsTest.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
test/jalview/structures/models/AAStructureBindingModelTest.java
Ben Soares [Thu, 4 Jun 2020 19:40:24 +0000 (20:40 +0100)]
JAL-3225 Minor change to building.md for flexmark, and html output files from the process, handy to have in repo for developers
Ben Soares [Thu, 4 Jun 2020 19:38:13 +0000 (20:38 +0100)]
JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.
Ben Soares [Tue, 2 Jun 2020 22:03:57 +0000 (23:03 +0100)]
JAL-3225 Using Gradle Git-Version plugin to set gitHash and gitBranch
Using Gradle Git-Version instead of exec to run git directly allows
buildship to successfully import the project into eclipse without a
command line git installed. Essential for development within Eclipse in
Windows without having to install either gradle or git as command line
tools.
soares [Mon, 1 Jun 2020 14:54:16 +0000 (15:54 +0100)]
JAL-3225 small fixes for building within Eclipse
Ben Soares [Tue, 2 Jun 2020 16:30:51 +0000 (17:30 +0100)]
JAL-3225 some fixes to build.gradle for working in Eclipse and not always changing doc/building.html
gmungoc [Mon, 1 Jun 2020 07:59:14 +0000 (08:59 +0100)]
JAL-3518 test result corrected
gmungoc [Mon, 1 Jun 2020 07:45:44 +0000 (08:45 +0100)]
JAL-3518 add alwaysRun = true [sigh]
gmungoc [Mon, 1 Jun 2020 07:30:08 +0000 (08:30 +0100)]
JAL-3518 more test coverage for structure commands
gmungoc [Fri, 29 May 2020 16:05:48 +0000 (17:05 +0100)]
JAL-2422 test updated
gmungoc [Fri, 29 May 2020 15:33:17 +0000 (16:33 +0100)]
Merge branch 'feature/JAL-3551Pymol' into develop
gmungoc [Fri, 29 May 2020 15:23:05 +0000 (16:23 +0100)]
JAL-3551 null pointer defence while structure files loading; comments
gmungoc [Thu, 28 May 2020 17:33:08 +0000 (18:33 +0100)]
JAL-3551 corrected Pymol open session command
gmungoc [Thu, 28 May 2020 17:27:31 +0000 (18:27 +0100)]
JAL-2422 correct ChimeraX save/open session commands; check for null
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
gmungoc [Tue, 26 May 2020 16:27:08 +0000 (17:27 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 26 May 2020 16:26:55 +0000 (17:26 +0100)]
JAL-1889 disable test failing on build server
soares [Tue, 26 May 2020 14:36:27 +0000 (15:36 +0100)]
Merge branch 'bug/JAL-3541_cloverReport_gradle_task_fails' into develop
soares [Tue, 26 May 2020 14:08:17 +0000 (15:08 +0100)]
JAL-3541 added a property/variable style comment to build.gradle
gmungoc [Tue, 26 May 2020 13:21:49 +0000 (14:21 +0100)]
JAL-3624 log when SIFTS mapping fails
gmungoc [Tue, 26 May 2020 12:38:55 +0000 (13:38 +0100)]
Merge branch 'feature/JAL-3624siftsInJS' into develop
gmungoc [Tue, 26 May 2020 11:51:17 +0000 (12:51 +0100)]
JAL-1761 pattern for structure viewer construction from project file
soares [Mon, 25 May 2020 23:14:15 +0000 (00:14 +0100)]
JAL-3541 selectively merged build.gradle and gradle.properties
Jim Procter [Mon, 25 May 2020 13:33:39 +0000 (14:33 +0100)]
JAL-3626 rescue automatic configuration of JALVIEW_VERSION from the RELEASE properties file, and exclusion of ‘examples’ from the windows installer.
Jim Procter [Mon, 2 Mar 2020 10:42:07 +0000 (10:42 +0000)]
JAL-3407 redact Java 8 incompatible '<>' with anonymous inner classes
gmungoc [Thu, 21 May 2020 17:27:28 +0000 (18:27 +0100)]
JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)
gmungoc [Thu, 21 May 2020 13:09:56 +0000 (14:09 +0100)]
JAL-2422 highlight ChimeraX selection (ChimeraX-1.0-rc-2020.05.21 +)
gmungoc [Wed, 20 May 2020 07:51:38 +0000 (08:51 +0100)]
JAL-3626 use Viewer.scriptWait() to send Jmol commands (Bob Hanson)
gmungoc [Tue, 19 May 2020 17:27:40 +0000 (18:27 +0100)]
JAL-3621 corrected sequence feature sort and test
gmungoc [Tue, 19 May 2020 17:27:40 +0000 (18:27 +0100)]
JAL-3621 corrected sequence feature sort and test
gmungoc [Tue, 19 May 2020 16:27:32 +0000 (17:27 +0100)]
Merge branch 'develop' into feature/JAL-3551Pymol
Conflicts:
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java
src/jalview/gui/AppJmol.java
src/jalview/gui/AppJmolBinding.java
src/jalview/gui/ChimeraViewFrame.java
src/jalview/gui/StructureViewerBase.java
src/jalview/jbgui/GPreferences.java
src/jalview/jbgui/GStructureViewer.java
src/jalview/project/Jalview2XML.java
gmungoc [Tue, 19 May 2020 10:50:41 +0000 (11:50 +0100)]
JAL-3624 use temp file for SIFT download in JS, correct unmarshalling
gmungoc [Mon, 18 May 2020 15:01:54 +0000 (16:01 +0100)]
JAL-3463 avoid Thread.sleep() as not supported in SwingJS
gmungoc [Mon, 18 May 2020 14:57:13 +0000 (15:57 +0100)]
JAL-3621 update to intervalstore v1.1
gmungoc [Mon, 18 May 2020 10:01:29 +0000 (11:01 +0100)]
JAL-3529 test updated for revised signature of getDBRefs()
gmungoc [Mon, 18 May 2020 09:59:52 +0000 (10:59 +0100)]
Merge branch 'Jalview-JS/develop' into develop
Conflicts:
build.gradle
src/jalview/gui/PopupMenu.java
src/jalview/io/SequenceAnnotationReport.java
src/jalview/io/StockholmFile.java
src/jalview/util/DBRefUtils.java
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
gmungoc [Mon, 18 May 2020 08:39:55 +0000 (09:39 +0100)]
JAL-3613 remove debug code committed in error
gmungoc [Fri, 15 May 2020 16:56:17 +0000 (17:56 +0100)]
JAL-2422 JAL-3551 unit tests updated for code changes
gmungoc [Fri, 15 May 2020 16:48:57 +0000 (17:48 +0100)]
JAL-3619 default silently to Jmol if viewerType absent (Jalview < 2.9)
gmungoc [Fri, 15 May 2020 07:43:26 +0000 (08:43 +0100)]
JAL-3551 pull up Close Viewer dialog to base class
gmungoc [Fri, 15 May 2020 06:30:28 +0000 (07:30 +0100)]
Merge branch 'feature/JAL-3551Pymol' into feature/JAL-2422ChimeraX
gmungoc [Fri, 15 May 2020 06:29:55 +0000 (07:29 +0100)]
JAL-3551 raise label on ('highlight') structure residue (wip)
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.
gmungoc [Tue, 12 May 2020 13:20:15 +0000 (14:20 +0100)]
JAL-3518 tidy method, remove obsolete comment
gmungoc [Tue, 12 May 2020 09:37:41 +0000 (10:37 +0100)]
JAL-3518 failsafe check for null Jmol filename while loading files
gmungoc [Mon, 11 May 2020 14:56:55 +0000 (15:56 +0100)]
JAL-3551 concatenate colour by sequence commands for all except PyMOL
gmungoc [Mon, 11 May 2020 13:12:03 +0000 (14:12 +0100)]
JAL-2422 JAL-3551 viewer text/variables generalised, Pymol paths added
gmungoc [Mon, 11 May 2020 10:42:56 +0000 (11:42 +0100)]
JAL-2422 ChimeraX paths (versions up to 1.0) added for Windows
gmungoc [Mon, 11 May 2020 09:14:47 +0000 (10:14 +0100)]
JAL-1333 additional Chimera versions for Windows installation paths
gmungoc [Mon, 11 May 2020 08:32:57 +0000 (09:32 +0100)]
JAL-2422 restore saved ChimeraX session from project
gmungoc [Fri, 1 May 2020 11:36:58 +0000 (12:36 +0100)]
JAL-3613 check sequence overlap when matching search results
gmungoc [Thu, 30 Apr 2020 10:50:27 +0000 (11:50 +0100)]
JAL-3551 save structure viewer session refactorings, PyMol added
gmungoc [Thu, 30 Apr 2020 10:47:39 +0000 (11:47 +0100)]
JAL-3551 tidied error handling for HTTP request
gmungoc [Sat, 25 Apr 2020 09:09:29 +0000 (10:09 +0100)]
Merge branch 'develop' into feature/JAL-3551Pymol
soares [Wed, 22 Apr 2020 19:58:55 +0000 (20:58 +0100)]
JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used
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 20:19:16 +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 17:23:46 +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 17:03:45 +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 13:16:17 +0000 (14:16 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
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
gmungoc [Tue, 21 Apr 2020 13:03:35 +0000 (14:03 +0100)]
JAL-3210 try adding setup method to unit test failing on server...
gmungoc [Tue, 21 Apr 2020 11:34:13 +0000 (12:34 +0100)]
JAL-1889 corrected wait for consensus to be calculated
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
Jim Procter [Tue, 21 Apr 2020 10:58:30 +0000 (11:58 +0100)]
Merge branch 'bug/JAL-3567virtualFeatureCoordinates' into develop
Jim Procter [Tue, 21 Apr 2020 10:48:44 +0000 (11:48 +0100)]
JAL-367 code tidy
Jim Procter [Tue, 21 Apr 2020 10:48:35 +0000 (11:48 +0100)]
JAL-3567 translated rather than imputed peptide
gmungoc [Tue, 21 Apr 2020 09:59:19 +0000 (10:59 +0100)]
JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies
Ben Soares [Tue, 21 Apr 2020 00:11:04 +0000 (01:11 +0100)]
JAL-3602 Added configuration for enforced use of UTF-8 for creating the
core js files and also in the closure-compiler.
gmungoc [Fri, 17 Apr 2020 13:00:10 +0000 (14:00 +0100)]
JAL-3567 unit tests for linked feature tooltips
BobHanson [Fri, 17 Apr 2020 00:19:45 +0000 (19:19 -0500)]
added .gitignore paths
I need these until I fully grasp the ways that gradle works.
BobHanson [Thu, 16 Apr 2020 19:08:11 +0000 (14:08 -0500)]
JAL-3587 Load Project bug
Fixed 2019.01.24 in Applet branch.
commit
db8caac49ea663fbc2b8b78f7eb2e6ae893f40da
didn't have a JAL number. My mistake.
gmungoc [Thu, 16 Apr 2020 17:43:21 +0000 (18:43 +0100)]
JAL-3567 adjust layout of linked feature report, unit test
gmungoc [Thu, 16 Apr 2020 16:37:46 +0000 (17:37 +0100)]
JAL-3567 added 'imputed by Jalview' to protein consequence in report
gmungoc [Thu, 16 Apr 2020 15:11:23 +0000 (16:11 +0100)]
JAL-3567 report mapped location for virtual features in tooltip etc
Jim Procter [Tue, 14 Apr 2020 15:38:39 +0000 (16:38 +0100)]
JAL-3407 JAL-3529 release notes
Jim Procter [Tue, 14 Apr 2020 15:33:50 +0000 (16:33 +0100)]
Merge branch 'bug/JAL-3529_uniprotidsinstockholm' into develop
Jim Procter [Tue, 14 Apr 2020 15:33:22 +0000 (16:33 +0100)]
JAL-3529 revert ordering of DBRef addition so it reflects situation after Pfam import </picky>
Jim Procter [Tue, 14 Apr 2020 12:50:54 +0000 (13:50 +0100)]
JAL-3597 improved Memory test suite by detecting base memory usage rather than assuming it is constant for each release.
Jim Procter [Tue, 14 Apr 2020 12:21:38 +0000 (13:21 +0100)]
JAL-3407 release date set to 16th April, known issue report for JAL-3574
Jim Procter [Tue, 14 Apr 2020 11:25:20 +0000 (12:25 +0100)]
Merge branch 'testing/JAL-3577_jalviewversion_autoset_fixed' into develop
gmungoc [Tue, 14 Apr 2020 08:26:14 +0000 (09:26 +0100)]
JAL-3583 remove debug logging, Javadoc added
gmungoc [Mon, 13 Apr 2020 15:42:42 +0000 (16:42 +0100)]
JAL-3574 test coverage corners
gmungoc [Mon, 13 Apr 2020 11:45:38 +0000 (12:45 +0100)]
JAL-3574 Matcher with integer/long value pattern (e.g. VCF POS locus)
gmungoc [Sun, 12 Apr 2020 14:43:21 +0000 (15:43 +0100)]
JAL-3596 change redacted
gmungoc [Sun, 12 Apr 2020 12:24:24 +0000 (13:24 +0100)]
JAL-3596 don't draw text over features if Show Text is unselected
gmungoc [Sun, 12 Apr 2020 11:51:12 +0000 (12:51 +0100)]
JAL-3583 consistent last[Formatted]Tooltip, show once only per residue
git://source.jalview.org / jalview.git / log