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

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JAL-3067 Initial preparation.

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Revert "Revert "JAL-3032 net.sf.j2s.core_3.2.1 upgrade""

This reverts commit 75ce39c3308a69bafc2e7c5514e44de22dd3d6f0.

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Revert "JAL-3032 net.sf.j2s.core_3.2.1 upgrade"

This reverts commit c9810b8cc443bd2ccd8c42b7318c68f6ae463f47.

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JAL-3032 net.sf.j2s.core_3.2.1 upgrade

- project build command back to org.eclipse.jdt.core.javabuilder

- uses JDT CompilationParticipant extension instead of a massive

specialized builder

- solves the Eclipse Photon (non)incremental build problem

- stamps transpiler version into trailer on each .js file

- best (but not critical) to use -clean option when starting Eclipse

after adding this new version of the transpiler.

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

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proof of concept for passing tree data to archaeopteryx

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JAL-1807 add j2s nature to project

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JAL-1807 fixing the Jalview git project name

JAL-1807 - change project name to Jalview Desktop to make it clearer in eclipse workspace

Jalview builds sucessfully and runs from eclipse

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Add support RNAML format

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Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop conflicts due to refactoring according to JAL-972, JAL-968, JAL-968 Conflicts: .classpath examples/appletParameters.html src/jalview/appletgui/AlignFrame.java src/jalview/appletgui/AlignViewport.java src/jalview/datamodel/SequenceGroup.java src/jalview/gui/AlignFrame.java src/jalview/gui/AlignViewport.java src/jalview/jbgui/GAlignFrame.java

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groovy tools update

update groovy bits

groovy nature not needed in project

added notes on third party library licencing and updated netbeans builder library deps

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