Ben Soares [Thu, 25 Apr 2019 16:25:50 +0000 (17:25 +0100)]
JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this in to eclipse classpath generation
Jalview Build Box [Thu, 25 Apr 2019 14:28:13 +0000 (15:28 +0100)]
Merge branch 'bug/JAL-3224_getdown_changed_to_unpack_tgz_resources' into task/JAL-3234_211_codesigning
Jalview Build Box [Thu, 25 Apr 2019 14:17:46 +0000 (15:17 +0100)]
JAL-3234 enable codesigning and executable-post-processor for install4j
Jalview Build Box [Thu, 25 Apr 2019 14:14:54 +0000 (15:14 +0100)]
JAL-3234 Gradle properties for signing: OSX_KEYSTORE, OSX_KEYPASS, JSIGN_SH
Ben Soares [Thu, 25 Apr 2019 13:59:38 +0000 (14:59 +0100)]
JAL-3224 JAL-3225 Some fixes in install4j template and build.gradle, and a correction of the Policy code in Jalview.java that I messed up earlier
Ben Soares [Thu, 25 Apr 2019 11:47:51 +0000 (12:47 +0100)]
JAL-3224 JAL-3225 To be compatible with install4j bundled JRE on windows, have changed all the java_vm folder references to jre in getdown jars too. Install4j Windows media now bundles a JRE (into this location) so it can launch install4j installer too. Java 11 installers working on Windows, but Java 1.8 complaining about com.sun.xml.ws.policy.Policy not found.
Ben Soares [Thu, 25 Apr 2019 01:02:49 +0000 (02:02 +0100)]
JAL-3224 JAL-3225 Added lines to check for updates to getdown-launcher.jar into Jalview. Put getdown-core into Jalview libs instead of getdown-launcher (enables update of getdown-launcher). Adjusted Eclipse to not error on use of com.sun.management.OperatingSystemMXBean.
Ben Soares [Thu, 25 Apr 2019 00:04:01 +0000 (01:04 +0100)]
JAL-3224 Tidied up Network installers in install4j template. Moved getdown-launcher.jar into dist (needed by Jalview anyway)
Ben Soares [Wed, 24 Apr 2019 22:28:28 +0000 (23:28 +0100)]
JAL-3224 minor fix for build.gradle and gradle eclipse
Jim Procter [Wed, 24 Apr 2019 19:29:32 +0000 (20:29 +0100)]
Merge branch 'task/JAL-3225_Integration_Gradle_building_into_Eclipse' into bug/JAL-3224_getdown_changed_to_unpack_tgz_resources
Jim Procter [Wed, 24 Apr 2019 15:44:04 +0000 (16:44 +0100)]
JAL-1929 JAL-3224 java 8 and java 11 specific getdown jre sets
Jim Procter [Wed, 24 Apr 2019 14:59:20 +0000 (15:59 +0100)]
JAL-1929 JAL-3224 JRE getdown URLs must be relative to host of getdown app base
Jim Procter [Tue, 23 Apr 2019 17:00:53 +0000 (18:00 +0100)]
JAL-3130 add JAVA_VERSION to shadowJar classifier so artifacts are distinct
Jim Procter [Tue, 23 Apr 2019 16:41:11 +0000 (17:41 +0100)]
JAL-3130 make sure only libDistDir/*.jar are added to the runtime classpath in shadowJar and makeDist
Jim Procter [Tue, 23 Apr 2019 15:33:24 +0000 (16:33 +0100)]
Merge branch 'develop' into bug/JAL-3224_getdown_changed_to_unpack_tgz_resources
Jim Procter [Tue, 23 Apr 2019 11:37:34 +0000 (12:37 +0100)]
JAL-1929 JAL-3224 getdown artefacts staged as getdown/website/${JAVA_VERSION}/...
Jim Procter [Tue, 23 Apr 2019 11:14:12 +0000 (12:14 +0100)]
JAL-1929 JAL-3224 getdown channel structure is {build/release version channel}/{JVM}
hansonr [Tue, 23 Apr 2019 03:48:49 +0000 (22:48 -0500)]
[JAL-3226] problem that JavaScript (or Java) may consolidate multiple
repaint() requests in unpredictable ways. In this case, the issue was
that in response to a CTRL-C/CTRL-V paste request, in Java a fast
repaint request preceded two full requests, thus resulting
in a full request for paint. In constrast, in JavaScript, the three
requests were bundled together into one, so the fastPaint flag was
still present for the second and third request.
This resulted in incomplete painting.
The solution was to set seqCanvas.fastPaint and idCanvas.fastPaint false
in PaintRefresher when the target to be painted is one of those two
components.
BH 2019.04.22
hansonr [Mon, 22 Apr 2019 17:10:09 +0000 (12:10 -0500)]
update of SwingJS -- no changes known.
Jim Procter [Mon, 22 Apr 2019 13:01:39 +0000 (14:01 +0100)]
JAL-3224 JAL-3196 still trying to specify projectFile property for install4j (still!)
Jim Procter [Mon, 22 Apr 2019 12:53:58 +0000 (13:53 +0100)]
JAL-3224 JAL-3196 still trying to specify projectFile property for install4j
Jim Procter [Mon, 22 Apr 2019 12:49:35 +0000 (13:49 +0100)]
JAL-3224 JAL-3196 specify file object in projectFile property for install4j task
Jim Procter [Mon, 22 Apr 2019 12:39:47 +0000 (13:39 +0100)]
JAL-3130 JAL-3224 patch URL paths to point to jalview.org/getdown/jpre/... for JREs
Jim Procter [Mon, 22 Apr 2019 12:25:44 +0000 (13:25 +0100)]
JAL-3130 provide absolute module path as J11 compile argument, and drop unneeded modules srcSet resource
Jim Procter [Mon, 22 Apr 2019 11:46:48 +0000 (12:46 +0100)]
Merge branch 'jims/JAL-3130_Java11_Gradle_publishing' into bug/JAL-3224_getdown_changed_to_unpack_tgz_resources
gmungoc [Fri, 10 Nov 2017 13:45:50 +0000 (13:45 +0000)]
JAL-2791 tailored message if find fails on selection region
hansonr [Thu, 18 Apr 2019 18:15:55 +0000 (13:15 -0500)]
minor code clean up
hansonr [Thu, 18 Apr 2019 18:15:24 +0000 (13:15 -0500)]
minor code clean up
hansonr [Thu, 18 Apr 2019 17:59:40 +0000 (12:59 -0500)]
// BH 2018.04.18 comment: addNotify() is not appropriate here. We
// are not changing ancestors, and keyboard action listeners do
// not need to be reset. addNotify() is a very expensive operation,
// requiring a full re-layout of all parents and children.
// Note in JComponent:
// This method is called by the toolkit internally and should
// not be called directly by programs.
// I note that addNotify() is called in several areas of Jalview.
hansonr [Thu, 18 Apr 2019 17:55:55 +0000 (12:55 -0500)]
Adds check for gap padding to disallow fast paint upon pasting if
alignment has been modified.
hansonr [Thu, 18 Apr 2019 17:54:46 +0000 (12:54 -0500)]
removes unnecessary clearFastPaint
hansonr [Thu, 18 Apr 2019 17:54:08 +0000 (12:54 -0500)]
Corrects incorrect calls to ViewportRanges.setEndSeq()
This function has the limit of height - 1, not height. Also adds safety
for start < 0 in ViewportRanges.setEndSeq();
hansonr [Thu, 18 Apr 2019 15:03:30 +0000 (10:03 -0500)]
pushing again, just comments
hansonr [Thu, 18 Apr 2019 14:32:42 +0000 (09:32 -0500)]
hack for fastpaint Java bug upshifting one line after a sequence
selection paste. Covered in Java by a full paint by ConsensusThread.
gmungoc [Thu, 18 Apr 2019 14:32:37 +0000 (15:32 +0100)]
JAL-1793 basic help text for VCF option
gmungoc [Thu, 18 Apr 2019 14:17:45 +0000 (15:17 +0100)]
JAL-3111 additional release notes
gmungoc [Thu, 18 Apr 2019 12:24:42 +0000 (13:24 +0100)]
JAL-3111 small simplification of table tags, valign top
gmungoc [Thu, 18 Apr 2019 12:08:26 +0000 (13:08 +0100)]
JAL-3111 release notes first pass complete
Ben Soares [Thu, 18 Apr 2019 12:02:11 +0000 (13:02 +0100)]
JAL-3130 moved jar needed for getdown to libs (not a module)
hansonr [Thu, 18 Apr 2019 11:53:00 +0000 (06:53 -0500)]
reverting seqPanel.seqCanvas.clearFastPaint();
Ben Soares [Thu, 18 Apr 2019 11:37:00 +0000 (12:37 +0100)]
JAL-3224 Removed JREs (these now need to be in ~/buildtools/jre/openjdk-java_vm/...). Moved install4j config to utils. Made install4j template file (gradle will edit this correctly). Fixed symbolic link in bundled MacOS JRE problem. Added getdown launcher with .tgz unbundling support [currently broken].
gmungoc [Thu, 18 Apr 2019 11:36:53 +0000 (12:36 +0100)]
JAL-2620 updated help page to mention alternative genetic code tables
gmungoc [Thu, 18 Apr 2019 08:36:57 +0000 (09:36 +0100)]
Merge branch 'develop' into Jalview-JS/develop
gmungoc [Thu, 18 Apr 2019 08:36:28 +0000 (09:36 +0100)]
JAL-3193 dbSource always "ENSEMBL"
gmungoc [Thu, 18 Apr 2019 08:31:17 +0000 (09:31 +0100)]
Merge branch 'develop' into Jalview-JS/develop
hansonr [Thu, 18 Apr 2019 03:54:33 +0000 (22:54 -0500)]
explicit Hashtable objects
hansonr [Thu, 18 Apr 2019 03:53:59 +0000 (22:53 -0500)]
adds an explicit clearing of the SeqCanvas fastPaint flag upon viewport
adjustment
gmungoc [Wed, 17 Apr 2019 15:34:58 +0000 (16:34 +0100)]
JAL-3026 fix bug loading Jalview Project (in Java)
Jim Procter [Wed, 17 Apr 2019 14:34:59 +0000 (15:34 +0100)]
JAL-3111 fix 2.11 html anchor in docs
Jim Procter [Wed, 17 Apr 2019 14:32:58 +0000 (15:32 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 17 Apr 2019 14:32:36 +0000 (15:32 +0100)]
JAL-3111 Jalview 2.11 what’s New and estimated release date
Jim Procter [Wed, 17 Apr 2019 14:32:07 +0000 (15:32 +0100)]
JAL-3111 tweak PCA documentation
Jim Procter [Wed, 17 Apr 2019 12:53:16 +0000 (13:53 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211
gmungoc [Wed, 17 Apr 2019 10:48:28 +0000 (11:48 +0100)]
Merge branch 'develop' into Jalview-JS/develop
Ben Soares [Wed, 17 Apr 2019 00:59:32 +0000 (01:59 +0100)]
JAL-3224 Add commons-compress-1.18.jar
Ben Soares [Wed, 17 Apr 2019 00:33:02 +0000 (01:33 +0100)]
JAL-3224 Bundling appropriate Mac OS/Windows JRE as java_vm in install4j
Ben Soares [Wed, 17 Apr 2019 00:04:19 +0000 (01:04 +0100)]
JAL-3224 New version of getdown which will cope with unpacking .tgz resources, specifically for the java_vm and symbolic links within
Ben Soares [Tue, 16 Apr 2019 23:45:47 +0000 (00:45 +0100)]
JAL-3130 moved resources/install4j to utils/install4j
hansonr [Tue, 16 Apr 2019 22:29:07 +0000 (17:29 -0500)]
better resource loading/file caching
hansonr [Tue, 16 Apr 2019 22:28:14 +0000 (17:28 -0500)]
caching of DnD files dropped
hansonr [Tue, 16 Apr 2019 21:07:20 +0000 (16:07 -0500)]
jmol-app updated for SwingJS ZipTools upgrade
hansonr [Tue, 16 Apr 2019 21:06:36 +0000 (16:06 -0500)]
localizes Thread colourby so that it does not cause ThreadStateException
in Java
hansonr [Tue, 16 Apr 2019 21:05:41 +0000 (16:05 -0500)]
comments only
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
hansonr [Tue, 16 Apr 2019 13:39:31 +0000 (08:39 -0500)]
missing check for JavaScript in client response for String (Java) vs.
Map (JavaScript) -- since JavaScript has already done the conversion to
a Map and needs no further JSON parsing.
Jim Procter [Tue, 16 Apr 2019 13:28:44 +0000 (14:28 +0100)]
JAL-3130 JAL-1889 report absolute paths for CommandLineTests
hansonr [Tue, 16 Apr 2019 13:20:31 +0000 (08:20 -0500)]
unused old SwingJS dependencies
hansonr [Tue, 16 Apr 2019 13:16:30 +0000 (08:16 -0500)]
unused old SwingJS dependencies
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
hansonr [Tue, 16 Apr 2019 12:34:10 +0000 (07:34 -0500)]
Adds _j2sclasslist.txt to SwingJS distribution; fixes missing
menuListener
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
gmungoc [Tue, 16 Apr 2019 11:48:31 +0000 (12:48 +0100)]
Merge branch 'bug/JAL-3218scalePanelPopups' into develop
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'
gmungoc [Mon, 15 Apr 2019 15:52:19 +0000 (16:52 +0100)]
JAL-3193 no separatge EnsemblGenomes source in SequenceFetcher
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
gmungoc [Mon, 15 Apr 2019 08:47:50 +0000 (09:47 +0100)]
Merge branch 'develop' into Jalview-JS/develop
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
Jim Procter [Wed, 10 Apr 2019 13:56:32 +0000 (14:56 +0100)]
JAL-3033 and more classes for examples core
Jim Procter [Tue, 9 Apr 2019 13:23:56 +0000 (14:23 +0100)]
JAL-3033 jalview.org/jalview-js/JalviewJS.shtml?open%20http://www.jalview.org/examples/uniref50.fa
hansonr [Tue, 9 Apr 2019 04:41:36 +0000 (23:41 -0500)]
JTable improvements
- prevents loss of tool tip when clicking or editing
- corrects offset of center label in variable color option
- speed somewhat improved
hansonr [Tue, 9 Apr 2019 04:39:28 +0000 (23:39 -0500)]
better comment regarding setting recognized ajax-enabled sites
hansonr [Tue, 9 Apr 2019 04:38:42 +0000 (23:38 -0500)]
Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into Jalview-JS/develop
hansonr [Tue, 9 Apr 2019 04:38:21 +0000 (23:38 -0500)]
code formatting only