jalview.git
5 years agoJAL-3210 updated Jmol library in j11lib, j8lib
gmungoc [Mon, 27 May 2019 09:46:23 +0000 (10:46 +0100)]
JAL-3210 updated Jmol library in j11lib, j8lib

5 years agoJAL-3210 delete old package post merge
gmungoc [Fri, 24 May 2019 10:32:55 +0000 (11:32 +0100)]
JAL-3210 delete old package post merge

5 years agoMerge branch 'develop' into trialMerge
gmungoc [Fri, 24 May 2019 10:31:34 +0000 (11:31 +0100)]
Merge branch 'develop' into trialMerge

Conflicts:
.classpath
.project
.settings/org.eclipse.jdt.core.prefs
.settings/org.eclipse.jdt.groovy.core.prefs
.settings/org.eclipse.jdt.ui.prefs
build.xml
src/MCview/AppletPDBCanvas.java
src/MCview/Atom.java
src/MCview/PDBCanvas.java
src/jalview/appletgui/EmbmenuFrame.java
src/jalview/appletgui/OverviewPanel.java
src/jalview/appletgui/SeqPanel.java
src/jalview/bin/Jalview.java
src/jalview/ext/paradise/Annotate3D.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/Desktop.java
src/jalview/gui/FeatureRenderer.java
src/jalview/gui/FeatureTypeSettings.java
src/jalview/io/FileLoader.java
src/jalview/jbgui/GDesktop.java
src/jalview/util/ImageMaker.java
src/jalview/util/Platform.java

5 years agoAdded to index to allow merge
gmungoc [Thu, 23 May 2019 10:07:19 +0000 (11:07 +0100)]
Added to index to allow merge

5 years agoUpdated to match develop to allow merge
gmungoc [Thu, 23 May 2019 10:06:40 +0000 (11:06 +0100)]
Updated to match develop to allow merge

5 years agoJAL-3111 help file spelling correction
gmungoc [Wed, 22 May 2019 08:41:41 +0000 (09:41 +0100)]
JAL-3111  help file spelling correction

5 years agoJAL-3273 small correction to expected result calculation
gmungoc [Tue, 21 May 2019 16:45:40 +0000 (17:45 +0100)]
JAL-3273 small correction to expected result calculation

5 years agoMerge branch 'task/JAL-3247_Install4j_improvements' into develop
Jim Procter [Mon, 13 May 2019 15:53:08 +0000 (16:53 +0100)]
Merge branch 'task/JAL-3247_Install4j_improvements' into develop

5 years agoMerge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into task/JAL...
Ben Soares [Mon, 13 May 2019 15:01:14 +0000 (16:01 +0100)]
Merge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into task/JAL-3247_Install4j_improvements

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 agoMerge branch 'task/JAL-3246_local_getdown_files' into develop
Jim Procter [Fri, 10 May 2019 16:41:37 +0000 (17:41 +0100)]
Merge branch 'task/JAL-3246_local_getdown_files' into develop

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 agoMerge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into develop
Jim Procter [Fri, 10 May 2019 16:21:16 +0000 (17:21 +0100)]
Merge branch 'task/JAL-3236_install4j_linux_unix_userland_installers' into develop

5 years agoJAL-3236 Added unixInstaller to install4jMediaTypes in gradle.properties
Ben Soares [Thu, 9 May 2019 19:14:13 +0000 (20:14 +0100)]
JAL-3236 Added unixInstaller to install4jMediaTypes in gradle.properties

5 years agoMerge branch 'task/JAL-3246_local_getdown_files' into develop
Jim Procter [Thu, 9 May 2019 16:19:45 +0000 (17:19 +0100)]
Merge branch 'task/JAL-3246_local_getdown_files' into develop

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-3240 known issue for release notes
gmungoc [Mon, 6 May 2019 08:49:45 +0000 (09:49 +0100)]
JAL-3240 known issue for release notes

5 years agoJAL-3239 release note
gmungoc [Mon, 6 May 2019 08:23:18 +0000 (09:23 +0100)]
JAL-3239 release note

5 years agoJAL-3244 release note
gmungoc [Mon, 6 May 2019 08:21:40 +0000 (09:21 +0100)]
JAL-3244 release note

5 years agoMerge remote-tracking branch 'origin/bug/JAL-3239monospacedEps' into develop
gmungoc [Mon, 6 May 2019 08:18:52 +0000 (09:18 +0100)]
Merge remote-tracking branch 'origin/bug/JAL-3239monospacedEps' into develop

5 years agoJAL-3244 delete obsolete method
gmungoc [Mon, 6 May 2019 08:07:53 +0000 (09:07 +0100)]
JAL-3244 delete obsolete method

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-3239 draw EPS or SVG one character at a time (even monospaced) bug/JAL-3239monospacedEps
gmungoc [Thu, 2 May 2019 13:37:13 +0000 (14:37 +0100)]
JAL-3239 draw EPS or SVG one character at a time (even monospaced)

5 years agoMerge branch 'bug/JAL-3244jmolWindows' into develop
gmungoc [Thu, 2 May 2019 11:36:32 +0000 (12:36 +0100)]
Merge branch 'bug/JAL-3244jmolWindows' into develop

5 years agoJAL-3244 renamed Platform method for clarity bug/JAL-3244jmolWindows
gmungoc [Thu, 2 May 2019 11:34:40 +0000 (12:34 +0100)]
JAL-3244 renamed Platform method for clarity

5 years agoadding another getdown file (produced during a getdown build) to gitignore
Ben Soares [Thu, 2 May 2019 11:17:24 +0000 (12:17 +0100)]
adding another getdown file (produced during a getdown build) to gitignore

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 agoJAL-3244 ignore file path separator when comparing pdb file paths
gmungoc [Wed, 1 May 2019 16:04:16 +0000 (17:04 +0100)]
JAL-3244 ignore file path separator when comparing pdb file paths

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-3226 removal of superseded changes
gmungoc [Fri, 26 Apr 2019 09:20:31 +0000 (10:20 +0100)]
JAL-3226 removal of superseded changes

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"

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 ago[JAL-3226] problem that JavaScript (or Java) may consolidate multiple
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

5 years agoupdate of SwingJS -- no changes known.
hansonr [Mon, 22 Apr 2019 17:10:09 +0000 (12:10 -0500)]
update of SwingJS -- no changes known.

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