jalview.git
5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Fri, 26 Apr 2019 16:34:39 +0000 (17:34 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoAdded a unixInstaller and unixArchive media-type to the install4j template. unixArch...
Ben Soares [Fri, 26 Apr 2019 16:25:20 +0000 (17:25 +0100)]
Added a unixInstaller and unixArchive media-type to the install4j template.  unixArchive is now specified in the gradle.properties (unixInstaller can be added).

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
Ben Soares [Fri, 26 Apr 2019 15:23:55 +0000 (16:23 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

5 years agoRemoving old commented out 'org.gradle.java.home=' line from gradle.properties
Ben Soares [Fri, 26 Apr 2019 15:22:53 +0000 (16:22 +0100)]
Removing old commented out 'org.gradle.java.home=' line from gradle.properties

5 years agoMerge branch 'develop' into releases/Release_2_11_Branch
Jim Procter [Fri, 26 Apr 2019 14:14:12 +0000 (15:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_Branch

5 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Fri, 26 Apr 2019 14:11:47 +0000 (15:11 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 26 Apr 2019 13:55:07 +0000 (14:55 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

5 years agoJAL-2743 class Javadoc
gmungoc [Fri, 26 Apr 2019 13:53:42 +0000 (14:53 +0100)]
JAL-2743 class Javadoc

5 years agoJAL-2738 JAL-2743 properties to map VCF header to species or assembly
gmungoc [Fri, 26 Apr 2019 13:52:30 +0000 (14:52 +0100)]
JAL-2738 JAL-2743 properties to map VCF header to species or assembly

5 years agoAlso removing eclipse .project and .settings from the branch. Run 'gradle cleanEclip...
Ben Soares [Fri, 26 Apr 2019 13:13:13 +0000 (14:13 +0100)]
Also removing eclipse .project and .settings from the branch.  Run 'gradle cleanEclipse eclipse' to produce fresh new eclipse project files (and either 'Refresh' project in eclipse, or 'Import... -> Existing gradle project') or just run 'gradle eclipse' to keep some of your existing project settings.

5 years agoRemoving .classpath from this branch
Ben Soares [Fri, 26 Apr 2019 12:20:49 +0000 (13:20 +0100)]
Removing .classpath from this branch

5 years agoJAL-3150 examples/exampleFile.jvp for updated manual/tutorial exercises
Jim Procter [Fri, 26 Apr 2019 11:34:30 +0000 (12:34 +0100)]
JAL-3150 examples/exampleFile.jvp for updated manual/tutorial exercises

5 years agoJAL-3233 Added isAMac check for -Xdock:icon addition to Launcher command. Added a...
Ben Soares [Fri, 26 Apr 2019 10:59:34 +0000 (11:59 +0100)]
JAL-3233 Added isAMac check for -Xdock:icon addition to Launcher command. Added a process.waitFor() so Launcher doesn't background Jalview

5 years agoJAL-3010 borderless 'x' for "delete this filter condition"
gmungoc [Fri, 26 Apr 2019 09:17:09 +0000 (10:17 +0100)]
JAL-3010 borderless 'x' for "delete this filter condition"

Conflicts:
src/jalview/gui/FeatureTypeSettings.java

5 years agoJAL-2808 better tooltip 'delete this condition'
gmungoc [Fri, 26 Apr 2019 09:41:33 +0000 (10:41 +0100)]
JAL-2808 better tooltip 'delete this condition'

5 years agoJAL-3234 tidy up stdout on build
Jalview Build Box [Thu, 25 Apr 2019 17:29:13 +0000 (18:29 +0100)]
JAL-3234 tidy up stdout on build

5 years agoJAL-3234 allow gradle builds to run without having to specify keysigning variables...
Jalview Build Box [Thu, 25 Apr 2019 17:26:31 +0000 (18:26 +0100)]
JAL-3234 allow gradle builds to run without having to specify keysigning variables by rewriting install4j flags

5 years agoMerge branch 'task/JAL-3234_211_codesigning' into develop
Jalview Build Box [Thu, 25 Apr 2019 16:50:53 +0000 (17:50 +0100)]
Merge branch 'task/JAL-3234_211_codesigning' into develop
JAL-3225 JAL-3196 JAL-3179 JAL-3227 JAL-3228 JAL-3229 JAL-3007 JAL-3111 Jalview 2.11 gradle/Java 11 build is now main develop branch

5 years agoMerge branch 'bug/JAL-3224_getdown_changed_to_unpack_tgz_resources' into task/JAL...
Jalview Build Box [Thu, 25 Apr 2019 16:49:57 +0000 (17:49 +0100)]
Merge branch 'bug/JAL-3224_getdown_changed_to_unpack_tgz_resources' into task/JAL-3234_211_codesigning

5 years agoJAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this...
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

5 years agoMerge branch 'bug/JAL-3224_getdown_changed_to_unpack_tgz_resources' into task/JAL...
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

5 years agoJAL-3234 enable codesigning and executable-post-processor for install4j
Jalview Build Box [Thu, 25 Apr 2019 14:17:46 +0000 (15:17 +0100)]
JAL-3234 enable codesigning and executable-post-processor for install4j

5 years agoJAL-3234 Gradle properties for signing: OSX_KEYSTORE, OSX_KEYPASS, JSIGN_SH
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

5 years agoJAL-3224 JAL-3225 Some fixes in install4j template and build.gradle, and a correction...
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

5 years agoJAL-3224 JAL-3225 To be compatible with install4j bundled JRE on windows, have change...
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.

5 years agoJAL-3224 JAL-3225 Added lines to check for updates to getdown-launcher.jar into Jalvi...
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.

5 years agoJAL-3224 Tidied up Network installers in install4j template. Moved getdown-launcher...
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)

5 years agoJAL-3224 minor fix for build.gradle and gradle eclipse
Ben Soares [Wed, 24 Apr 2019 22:28:28 +0000 (23:28 +0100)]
JAL-3224 minor fix for build.gradle and gradle eclipse

5 years agoMerge branch 'task/JAL-3225_Integration_Gradle_building_into_Eclipse' into bug/JAL...
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

5 years agoJAL-1929 JAL-3224 java 8 and java 11 specific getdown jre sets
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

5 years agoJAL-1929 JAL-3224 JRE getdown URLs must be relative to host of getdown app base
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

5 years agoJAL-3130 add JAVA_VERSION to shadowJar classifier so artifacts are distinct
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

5 years agoJAL-3130 make sure only libDistDir/*.jar are added to the runtime classpath in shadow...
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

5 years agoMerge branch 'develop' into bug/JAL-3224_getdown_changed_to_unpack_tgz_resources
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

5 years agoJAL-1929 JAL-3224 getdown artefacts staged as getdown/website/${JAVA_VERSION}/...
Jim Procter [Tue, 23 Apr 2019 11:37:34 +0000 (12:37 +0100)]
JAL-1929 JAL-3224 getdown artefacts staged as getdown/website/${JAVA_VERSION}/...

5 years agoJAL-1929 JAL-3224 getdown channel structure is {build/release version channel}/{JVM}
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}

5 years agoJAL-3224 JAL-3196 still trying to specify projectFile property for install4j (still!)
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!)

5 years agoJAL-3224 JAL-3196 still trying to specify projectFile property for install4j
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

5 years agoJAL-3224 JAL-3196 specify file object in projectFile property for install4j task
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

5 years agoJAL-3130 JAL-3224 patch URL paths to point to www.jalview.org/getdown/jpre/... for...
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

5 years agoJAL-3130 provide absolute module path as J11 compile argument, and drop unneeded...
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

5 years agoMerge branch 'jims/JAL-3130_Java11_Gradle_publishing' into bug/JAL-3224_getdown_chang...
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

5 years agoJAL-2791 tailored message if find fails on selection region
gmungoc [Fri, 10 Nov 2017 13:45:50 +0000 (13:45 +0000)]
JAL-2791 tailored message if find fails on selection region

5 years agoJAL-1793 basic help text for VCF option
gmungoc [Thu, 18 Apr 2019 14:32:37 +0000 (15:32 +0100)]
JAL-1793 basic help text for VCF option

5 years agoJAL-3111 additional release notes
gmungoc [Thu, 18 Apr 2019 14:17:45 +0000 (15:17 +0100)]
JAL-3111 additional release notes

5 years agoJAL-3111 small simplification of table tags, valign top
gmungoc [Thu, 18 Apr 2019 12:24:42 +0000 (13:24 +0100)]
JAL-3111 small simplification of table tags, valign top

5 years agoJAL-3111 release notes first pass complete
gmungoc [Thu, 18 Apr 2019 12:08:26 +0000 (13:08 +0100)]
JAL-3111 release notes first pass complete

5 years agoJAL-3130 moved jar needed for getdown to libs (not a module)
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)

5 years agoJAL-3224 Removed JREs (these now need to be in ~/buildtools/jre/openjdk-java_vm/...
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].

5 years agoJAL-2620 updated help page to mention alternative genetic code tables
gmungoc [Thu, 18 Apr 2019 11:36:53 +0000 (12:36 +0100)]
JAL-2620 updated help page to mention alternative genetic code tables

5 years agoJAL-3193 dbSource always "ENSEMBL"
gmungoc [Thu, 18 Apr 2019 08:36:28 +0000 (09:36 +0100)]
JAL-3193 dbSource always "ENSEMBL"

5 years agoJAL-3111 fix 2.11 html anchor in docs
Jim Procter [Wed, 17 Apr 2019 14:34:59 +0000 (15:34 +0100)]
JAL-3111 fix 2.11 html anchor in docs

5 years agoMerge branch 'documentation/JAL-3111_release_211' into develop
Jim Procter [Wed, 17 Apr 2019 14:32:58 +0000 (15:32 +0100)]
Merge branch 'documentation/JAL-3111_release_211' into develop

5 years agoJAL-3111 Jalview 2.11 what’s New and estimated release date
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

5 years agoJAL-3111 tweak PCA documentation
Jim Procter [Wed, 17 Apr 2019 14:32:07 +0000 (15:32 +0100)]
JAL-3111 tweak PCA documentation

5 years agoMerge branch 'develop' into documentation/JAL-3111_release_211
Jim Procter [Wed, 17 Apr 2019 12:53:16 +0000 (13:53 +0100)]
Merge branch 'develop' into documentation/JAL-3111_release_211

5 years agoJAL-3224 Add commons-compress-1.18.jar
Ben Soares [Wed, 17 Apr 2019 00:59:32 +0000 (01:59 +0100)]
JAL-3224 Add commons-compress-1.18.jar

5 years agoJAL-3224 Bundling appropriate Mac OS/Windows JRE as java_vm in install4j
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

5 years agoJAL-3224 New version of getdown which will cope with unpacking .tgz resources, specif...
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

5 years agoJAL-3130 moved resources/install4j to utils/install4j
Ben Soares [Tue, 16 Apr 2019 23:45:47 +0000 (00:45 +0100)]
JAL-3130 moved resources/install4j to utils/install4j

5 years agoJAL-3130 tidy up system.output jims/JAL-3130_Java11_Gradle_publishing
Jim Procter [Tue, 16 Apr 2019 16:38:59 +0000 (17:38 +0100)]
JAL-3130 tidy up system.output

5 years agoJAL-3130 call Jalview via the Test JVM’s JAVA_HOME/bin/java
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

5 years agoJAL-3130 refactored ‘clover’ to ‘use_clover’ since clover is an ambiguous property...
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

5 years agoJAL-3130 JAL-1889 reportCurrentWorkingDirectory test to report absolute path when...
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

5 years agoJAL-3130 JAL-1889 report absolute paths for CommandLineTests
Jim Procter [Tue, 16 Apr 2019 13:28:44 +0000 (14:28 +0100)]
JAL-3130 JAL-1889 report absolute paths for CommandLineTests

5 years agoJAL-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

5 years agoJAL-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

5 years agoJAL-3196 change default are resource properties to http://www.jalview.org/getdown/jre
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

5 years agoMerge branch 'bug/JAL-3218scalePanelPopups' into develop
gmungoc [Tue, 16 Apr 2019 11:48:31 +0000 (12:48 +0100)]
Merge branch 'bug/JAL-3218scalePanelPopups' into develop

5 years agoReinstate imports from "JAL-1889 JAL-3130 patch broken tests" commit 05efc2ac3c6427a4...
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.

5 years agoJAL-1189 JAL-3130 patch broken tests
Jim Procter [Tue, 16 Apr 2019 09:33:42 +0000 (10:33 +0100)]
JAL-1189 JAL-3130 patch broken tests

5 years agoJAL-3130 Somewhere in the old libs the Jws2 client is working. Compile with Java...
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

5 years agoJAL-3130 Helper classes to take Class Exceptions when run in java 1.8 JRE out of...
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

5 years agoJAL-3130 some clover fixes for helplinks. Use 'gradle test -Pclover=true'
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'

5 years agoJAL-3193 no separatge EnsemblGenomes source in SequenceFetcher
gmungoc [Mon, 15 Apr 2019 15:52:19 +0000 (16:52 +0100)]
JAL-3193 no separatge EnsemblGenomes source in SequenceFetcher

5 years agoJAL-3130 adapted getdown src. attempt 2. first attempt failed due to cp'ed .git files
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

5 years agoJAL-3130 write clover.xml during cloverReport phase
Jim Procter [Sun, 14 Apr 2019 20:22:45 +0000 (21:22 +0100)]
JAL-3130 write clover.xml during cloverReport phase

5 years agoJAL-3130 make sure testng-results.xml is generated
Jim Procter [Sun, 14 Apr 2019 10:48:05 +0000 (11:48 +0100)]
JAL-3130 make sure testng-results.xml is generated

5 years agoJAL-3130 specify module list when launching new Jalview for CLI tests
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

5 years agoJAL-3130 instrument main and compile separately to test classes so Clover doesn’t...
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

5 years agoJAL-3130 gradle test now runs open clover 4.3.1 and new cloverReport task
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

5 years agoMerge branch 'develop' into task/JAL-3130_Java_11_investigations-getdown_src
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

5 years agoJAL-3130 ensure J11 libs/modules are added when building and running test suite
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

5 years agoJAL-3130 clean up eclipse class path for dependencies moved to j11lib
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

5 years agoJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
gmungoc [Wed, 10 Apr 2019 20:35:10 +0000 (21:35 +0100)]
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org

5 years agoJAL-3018 REST version updated to 10.0
gmungoc [Wed, 10 Apr 2019 20:20:22 +0000 (21:20 +0100)]
JAL-3018 REST version updated to 10.0

5 years agoJAL-3130 adapted getdown src
Ben Soares [Fri, 5 Apr 2019 17:01:18 +0000 (18:01 +0100)]
JAL-3130 adapted getdown src

5 years agoJAL-3130 This commit concentrates on the Mac OS X DMG app bundle, ensuring only one...
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

5 years agoJAL-3130 trying to be Java 1.8 source compatible -- not sure if this is ultimately...
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

5 years agoJAL-3130 JAL-3007 more files needed for getdown launcher
Ben Soares [Thu, 4 Apr 2019 10:09:04 +0000 (11:09 +0100)]
JAL-3130 JAL-3007 more files needed for getdown launcher

5 years agoJAL-3130 JAL-3007 improvements to gradle build
Ben Soares [Thu, 4 Apr 2019 10:08:07 +0000 (11:08 +0100)]
JAL-3130 JAL-3007 improvements to gradle build

5 years agoJAL-3021 show Sequence Details with cursor at top
gmungoc [Wed, 3 Apr 2019 15:43:19 +0000 (16:43 +0100)]
JAL-3021 show Sequence Details with cursor at top

5 years agoJAL-3218 allow both Hide and Reveal in scale panel popup menu bug/JAL-3218scalePanelPopups
gmungoc [Tue, 2 Apr 2019 13:10:45 +0000 (14:10 +0100)]
JAL-3218 allow both Hide and Reveal in scale panel popup menu

5 years agoJAL-3130 JAL-3007 Added gradle build for Java 11. Now in root jalview dir
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

5 years agoJAL-3130 JAL-3007 Added gradle build for Java 11 and additional taskbar icon change...
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

5 years agoJAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar
gmungoc [Fri, 29 Mar 2019 11:05:29 +0000 (11:05 +0000)]
JAL-3140 InstallAnywhere updated to intervalstore-v1.0.jar

5 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
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

5 years agoJAL-3140 intervalstore now v1.0 (public release)
gmungoc [Fri, 29 Mar 2019 10:30:51 +0000 (10:30 +0000)]
JAL-3140 intervalstore now v1.0 (public release)

5 years agoJAL-3111 Disable the pubapplet target in build.xml so cruisecontrol build can complete
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

5 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Thu, 28 Mar 2019 17:34:20 +0000 (17:34 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop