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JAL-3560 Java 11 fix on JAL-3563 moving j11lib set up to top

classpath ordering

- j11lib needs to be declared before j8lib for saaj and probably many

others.

- Jalview.java allows synchronization

- CommandLineOperations working; seems at least on Bob's machine process

with file writing termination does not equate with file.exists(); join

is returning too early? How can that be...

- Jalview2xmlTests back to correct answer and now working with

Jalview.setSynchronized(true);

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Java 11/Gradle 2.5 upgrade

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Java 11 integration;

-- compiler complaining about javax.xml module

Failed to resolve resource /.build_properties:

@swingjs/j2s/jalview/bin/Cache.js:164:24

transpiler was 3.2.9-v1 now 3.2.4.07 for net.miginfocom.swing.MigLayout

TypeError: C$.UNIT_MAP.put$TK$TV is not a function

-- some runtime errors involving resources

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Revert "JAL-3210 default eclipse .project .classpath and .settings/org.eclipse.jdt.core.prefs so Eclipse as IDE can import without gradle"

This reverts commit aaa5f22a4544c3e72b5d29ef2f319e55af8e14f7.

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JAL-3210 default eclipse .project .classpath and .settings/org.eclipse.jdt.core.prefs so Eclipse as IDE can import without gradle

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JAL-3210 removed eclipse project, classpath and core settings files from branch. Now generate these (once only) with 'gradle eclipse'.

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Merge branch 'develop' into Jalview-JS/develop

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/analysis/CrossRef.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/PopupMenu.java

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JAL-3397 impl.IntervalStore and nonc.IntervalStore unified api

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-3210 test commit

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JAL-3210 ben testing

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JAL-3210 ben testing

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JAL-3210 ben testing

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JAL-3210 ben testing

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JAL-3210 Merge branch 'develop' into trialMerge

Conflicts:

.classpath

.project

.settings/org.eclipse.jdt.core.prefs

.settings/org.eclipse.jdt.ui.prefs

build.xml

resources/lang/Messages_es.properties

src/MCview/AppletPDBCanvas.java

src/MCview/Atom.java

src/MCview/PDBCanvas.java

src/jalview/analysis/AAFrequency.java

src/jalview/appletgui/EmbmenuFrame.java

src/jalview/appletgui/OverviewPanel.java

src/jalview/appletgui/SeqPanel.java

src/jalview/bin/Cache.java

src/jalview/bin/Jalview.java

src/jalview/datamodel/DBRefEntry.java

src/jalview/datamodel/Sequence.java

src/jalview/ext/ensembl/EnsemblMap.java

src/jalview/ext/paradise/Annotate3D.java

src/jalview/fts/service/pdb/PDBFTSRestClient.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureRenderer.java

src/jalview/gui/FeatureTypeSettings.java

src/jalview/gui/WebserviceInfo.java

src/jalview/io/BackupFiles.java

src/jalview/io/FileLoader.java

src/jalview/jbgui/GDesktop.java

src/jalview/jbgui/GPreferences.java

src/jalview/project/Jalview2XML.java

src/jalview/util/ImageMaker.java

src/jalview/util/Platform.java

src/jalview/ws/SequenceFetcher.java

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Test file relocated to test/jalview/io.

Test file relocated to test/jalview/io.

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

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Can remove class Jalview$FeatureFetcher.

Can remove class Jalview$FeatureFetcher.

Removing .classpath from this branch

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.

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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.

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Merge branch 'task/JAL-3225_Integration_Gradle_building_into_Eclipse' into bug/JAL-3224_getdown_changed_to_unpack_tgz_resources

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JAL-3225 added resources as a src path

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JAL-3225 Removing /classes for eclipse (Eclipse uses bin/main)

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JAL-3225 I THINK I HAVE WON\! Run 'gradle cleanEclipse eclipse' to get a new set of eclipse .project, .classpath, .settings/\* files that should work. You might need to have a Java 11 linked to 'org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11/' in your Installed JREs and Java compliance.

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JAL-1929 JAL-3224 getdown artefacts staged as getdown/website/${JAVA_VERSION}/...

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JAL-3225 Custom classpath and project creation. Run 'gradle cleanEclipse eclipse' before launching eclipse. Refresh project.

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JAL-3225 fixed settings for Eclipse

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JAL-3225 Edited .project and .classpath, and adjusted build.gradle for running within eclipse [note, pwd is different -- use 'file' and not 'new File'\!]

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