jalview.git
5 years agoJAL-3247 nogradle option on this mac build/install helper script
Ben Soares [Mon, 13 May 2019 14:51:15 +0000 (15:51 +0100)]
JAL-3247 nogradle option on this mac build/install helper script

5 years agoJAL-3247 JAL-3254 JAL-3260 Fixed: JVL file jalview.apparg args. File association...
Ben Soares [Mon, 13 May 2019 14:17:24 +0000 (15:17 +0100)]
JAL-3247 JAL-3254 JAL-3260 Fixed: JVL file jalview.apparg args. File association problem in Windows NETWORK installer.

5 years agoJAL-3246 JAL-3247 Reworked JVL files as getdown.txt config with limitations
Ben Soares [Fri, 10 May 2019 16:39:24 +0000 (17:39 +0100)]
JAL-3246 JAL-3247 Reworked JVL files as getdown.txt config with limitations

5 years agoJAL-3247 JAL-3254 Ensure .jvp and .jvl appear first in File Associations list (visibl...
Ben Soares [Thu, 9 May 2019 16:04:06 +0000 (17:04 +0100)]
JAL-3247 JAL-3254 Ensure .jvp and .jvl appear first in File Associations list (visible in Windows installer)

5 years agoJAL-3247 JAL-3254 Fixed file association launch behaviour in getdown in Windows
Ben Soares [Thu, 9 May 2019 16:03:12 +0000 (17:03 +0100)]
JAL-3247 JAL-3254 Fixed file association launch behaviour in getdown in Windows

5 years agoJAL-3246 add -Pgetdown_local=true to use local files
Ben Soares [Wed, 8 May 2019 17:25:06 +0000 (18:25 +0100)]
JAL-3246 add -Pgetdown_local=true to use local files

5 years agoJAL-3247 JAL-3254 changing default location of jalview/io/FileFormat.java relative...
Ben Soares [Wed, 8 May 2019 16:35:31 +0000 (17:35 +0100)]
JAL-3247 JAL-3254 changing default location of jalview/io/FileFormat.java relative to the util/install4j dir

5 years agoJAL-3247 JAL-3254 Getdown now opening any files thrown at it by a file-association...
Ben Soares [Wed, 8 May 2019 16:33:45 +0000 (17:33 +0100)]
JAL-3247 JAL-3254 Getdown now opening any files thrown at it by a file-association double-click

5 years agoJAL-3247 JAL-3254 Automatically creating correct file association inserts for Info...
Ben Soares [Wed, 8 May 2019 16:18:22 +0000 (17:18 +0100)]
JAL-3247 JAL-3254 Automatically creating correct file association inserts for Info.plist and install4j installer

5 years agoJAL-3247 JAL-3254 Automatically creating correct file association inserts for Info...
Ben Soares [Wed, 8 May 2019 16:17:05 +0000 (17:17 +0100)]
JAL-3247 JAL-3254 Automatically creating correct file association inserts for Info.plist and install4j installer

5 years agoJAL-3247 Script to produce auto file association files for mac and windows installer...
Ben Soares [Wed, 8 May 2019 12:43:33 +0000 (13:43 +0100)]
JAL-3247 Script to produce auto file association files for mac and windows installer, and changes in build.gradle to read in the produced, and edited, auto files

5 years agoJAL-3247 Note in launcher.log when using a JVL file
Ben Soares [Wed, 8 May 2019 10:57:57 +0000 (11:57 +0100)]
JAL-3247 Note in launcher.log when using a JVL file

5 years agoJAL-3247 Changed JVL file to be a props file, with appbase=... required for the new...
Ben Soares [Tue, 7 May 2019 23:05:44 +0000 (00:05 +0100)]
JAL-3247 Changed JVL file to be a props file, with appbase=... required for the new appbase URL

5 years agoJAL-3247 Script to automatically install Jalview from the .dmg to /Applications
Ben Soares [Tue, 7 May 2019 21:49:38 +0000 (22:49 +0100)]
JAL-3247 Script to automatically install Jalview from the .dmg to /Applications

5 years agoJAL-3247 Auto generated file associations from jalview/io/FileFormat.java
Ben Soares [Tue, 7 May 2019 19:17:48 +0000 (20:17 +0100)]
JAL-3247 Auto generated file associations from jalview/io/FileFormat.java

5 years agoJAL-3247 Allowing 'file' protocol URL with empty domain in a .jvl file
Ben Soares [Mon, 6 May 2019 23:38:52 +0000 (00:38 +0100)]
JAL-3247 Allowing 'file' protocol URL with empty domain in a .jvl file

5 years agoJAL-3247 Code changes to getdown. Double click open of .jvp files in Windows and...
Ben Soares [Mon, 6 May 2019 16:06:29 +0000 (17:06 +0100)]
JAL-3247 Code changes to getdown. Double click open of .jvp files in Windows and macOS, and .jvl new appbase file working in macOS.

5 years agoJAL-3247 improvements
Ben Soares [Mon, 6 May 2019 13:54:23 +0000 (14:54 +0100)]
JAL-3247 improvements

5 years agoJAL-3247 Some getdown image file changes/tidying
Ben Soares [Mon, 6 May 2019 12:56:31 +0000 (13:56 +0100)]
JAL-3247 Some getdown image file changes/tidying

5 years agoJAL-3247 First attempt at getdown code to add macOS startup filenames to the appargs...
Ben Soares [Fri, 3 May 2019 23:03:55 +0000 (00:03 +0100)]
JAL-3247 First attempt at getdown code to add macOS startup filenames to the appargs as -open filename

5 years agoJAL-3247 Part way towards adding double-click opening in Jalview on .jvp file in...
Ben Soares [Fri, 3 May 2019 19:28:56 +0000 (20:28 +0100)]
JAL-3247 Part way towards adding double-click opening in Jalview on .jvp file in macOS

5 years agoJAL-3247 Improved file associations on macOS and Windows
Ben Soares [Thu, 2 May 2019 15:55:57 +0000 (16:55 +0100)]
JAL-3247 Improved file associations on macOS and Windows

5 years agoJAL-3247 jvp jvl File associations, JRE variablised, Windows-Userspace path default
Ben Soares [Thu, 2 May 2019 11:11:09 +0000 (12:11 +0100)]
JAL-3247 jvp jvl File associations, JRE variablised, Windows-Userspace path default

5 years agoFixed -Djvl=true in install4j JVM invocation
Ben Soares [Wed, 1 May 2019 16:36:52 +0000 (17:36 +0100)]
Fixed -Djvl=true in install4j JVM invocation

5 years agoExtra JVL file association in the installer. Shadowed gradle-launcher.jar and classpa...
Ben Soares [Wed, 1 May 2019 16:18:03 +0000 (17:18 +0100)]
Extra JVL file association in the installer. Shadowed gradle-launcher.jar and classpath adjusted in install4j template. 'jre' folder made a compiler variable in install4j template.

5 years agoMerge branch 'task/JAL-3243_PDB_free_text_error' into develop
Ben Soares [Wed, 1 May 2019 13:37:45 +0000 (14:37 +0100)]
Merge branch 'task/JAL-3243_PDB_free_text_error' into develop

Merging in JAL-3243 replacement .jar files for jersey and javax.ws.rs.

5 years agoJAL-3243 Replaced javax.ws jar compatible with jersey-*-1.19.1.jar task/JAL-3243_PDB_free_text_error
Ben Soares [Tue, 30 Apr 2019 17:05:49 +0000 (18:05 +0100)]
JAL-3243 Replaced javax.ws jar compatible with jersey-*-1.19.1.jar

5 years agoJAL-3196 Correcting the source for getdown (already corrected in util/install4j/insta...
Ben Soares [Tue, 30 Apr 2019 11:51:16 +0000 (12:51 +0100)]
JAL-3196 Correcting the source for getdown (already corrected in util/install4j/install4j_template.install4j and getdown/lib/getdown-launcher.jar)

5 years agoJAL-3241 simplified enum constructors for classloadability in Java 11
gmungoc [Tue, 30 Apr 2019 10:57:49 +0000 (11:57 +0100)]
JAL-3241 simplified enum constructors for classloadability in Java 11

5 years agoJAL-2738 JAL-2743 update unit test to match new VCF properties
gmungoc [Mon, 29 Apr 2019 14:17:45 +0000 (15:17 +0100)]
JAL-2738 JAL-2743 update unit test to match new VCF properties

5 years agoJAL-3003 help page mention EPS doesn't support transparency
gmungoc [Mon, 29 Apr 2019 13:47:30 +0000 (14:47 +0100)]
JAL-3003 help page mention EPS doesn't support transparency

5 years agoJAL-3236 see also previous commit - tweak the install4j template so our installers...
Jim Procter [Fri, 26 Apr 2019 16:47:35 +0000 (17:47 +0100)]
JAL-3236 see also previous commit - tweak the install4j template so our installers get built !

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' 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.