org.eclipse.jdt.core.prefs

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JAL-3253

sets setting for "unlikely argument type for collection" to warning; I

have set my workspace to error, but clearly it had not been like that,

because it found three errors. But now setting it to warning so that it

is not bothering me.

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

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JAL-3210 test commit

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JAL-3210 updating. no test

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JAL-3210 ben testing

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    ./org.eclipse.jdt.core.prefs
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JAL-3210 ben testing

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JAL-3210 ben testing

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    ./org.eclipse.jdt.core.prefs
JAL-3210 ben testing

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JAL-3210 ben testing

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

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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 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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    ./org.eclipse.jdt.core.prefs
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JAL-3225 fixed settings for Eclipse

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JAL-3225 Formatting when save

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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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JAL-1551 reinstate formatting and save actions (with Java 1.8 additions)

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nonfunctional testing directory - just so I can see how it compiles.

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Java2Script 3.2.2 upgrade

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JAL-3026 adds org.json.simple to srcjars and jsonsimple-site.zip

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JAL-2944: Allow structures to be opened in a specific structure view
JAL-2944: Allow structures to be opened in a specific structure view