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(parent: d8e8c74) | patch
Java 11 integration;
authorBobHanson <hansonr@stolaf.edu>
Wed, 18 Mar 2020 03:52:41 +0000 (22:52 -0500)
committerBobHanson <hansonr@stolaf.edu>
Wed, 18 Mar 2020 03:52:41 +0000 (22:52 -0500)
commit9f55415c9f8005e9dcd8243453883ff853fd5b76
treecc3cc21c500a45953f73e3eed3aaa7684d49c0e7tree | snapshot
parentd8e8c742b864e58406d13e21d124699a26b6492fcommit | diff
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
460 files changed:
.classpath diff | blob | history
.j2s diff | blob | history
.settings/org.eclipse.jdt.core.prefs diff | blob | history
dirs [new file with mode: 0644] blob
j11lib/FastInfoset.jar [new file with mode: 0644] blob
j11lib/JGoogleAnalytics_0.3.jar [new file with mode: 0644] blob
j11lib/Jmol-14.29.17-no_netscape.jar [new file with mode: 0644] blob
j11lib/VARNAv3-93.jar [new file with mode: 0644] blob
j11lib/VAqua5-patch.jar [new file with mode: 0644] blob
j11lib/apache-mime4j-0.6.jar [new file with mode: 0644] blob
j11lib/axis.jar [new file with mode: 0644] blob
j11lib/biojava-core-4.1.0.jar [new file with mode: 0644] blob
j11lib/biojava-ontology-4.1.0.jar [new file with mode: 0644] blob
j11lib/commons-codec-1.3.jar [new file with mode: 0644] blob
j11lib/commons-compress-1.18.jar [new file with mode: 0644] blob
j11lib/commons-discovery.jar [new file with mode: 0644] blob
j11lib/commons-logging-1.1.1.jar [new file with mode: 0644] blob
j11lib/getdown-core.jar [new file with mode: 0644] blob
j11lib/gmbal-api-only-MODULE.jar [new file with mode: 0644] blob
j11lib/groovy-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-ant-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-bsf-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-cli-commons-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-cli-picocli-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-console-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-datetime-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-dateutil-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-docgenerator-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-groovydoc-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-groovysh-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-jaxb-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-jmx-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-json-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-json-direct-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-jsr223-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-macro-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-nio-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-servlet-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-sql-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-swing-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-templates-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-test-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-test-junit5-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-testng-2.5.7.jar [new file with mode: 0644] blob
j11lib/groovy-xml-2.5.7.jar [new file with mode: 0644] blob
j11lib/htsjdk-2.12.0.jar [new file with mode: 0644] blob
j11lib/httpclient-4.0.3.jar [new file with mode: 0644] blob
j11lib/httpcore-4.0.1.jar [new file with mode: 0644] blob
j11lib/httpmime-4.0.3.jar [new file with mode: 0644] blob
j11lib/intervalstore-v1.0.jar [new file with mode: 0644] blob
j11lib/istack-commons-runtime.jar [new file with mode: 0644] blob
j11lib/jabaws-min-client-2.2.0.jar [new file with mode: 0644] blob
j11lib/java-json.jar [new file with mode: 0644] blob
j11lib/javax.activation-api-1.2.0.jar [new file with mode: 0644] blob
j11lib/javax.annotation-api-1.3.2.jar [new file with mode: 0644] blob
j11lib/javax.jws-api-1.1.jar [new file with mode: 0644] blob
j11lib/javax.servlet-api-4.0.1.jar [new file with mode: 0644] blob
j11lib/javax.xml.rpc-api-1.1.2.jar [new file with mode: 0644] blob
j11lib/javax.xml.soap-api-1.4.0.jar [new file with mode: 0644] blob
j11lib/jaxb-api-2.3.1.jar [new file with mode: 0644] blob
j11lib/jaxb-runtime-2.3.2.jar [new file with mode: 0644] blob
j11lib/jaxws-api-2.3.1.jar [new file with mode: 0644] blob
j11lib/jaxws-rt-java9.jar [new file with mode: 0644] blob
j11lib/jersey-client-1.19.4.jar [new file with mode: 0644] blob
j11lib/jersey-core-1.19.4.jar [new file with mode: 0644] blob
j11lib/jersey-json-1.19.4.jar [new file with mode: 0644] blob
j11lib/jetty-http-9.2.10.v20150310.jar [new file with mode: 0644] blob
j11lib/jetty-io-9.2.10.v20150310.jar [new file with mode: 0644] blob
j11lib/jetty-server-9.2.10.v20150310.jar [new file with mode: 0644] blob
j11lib/jetty-util-9.2.10.v20150310.jar [new file with mode: 0644] blob
j11lib/jfreesvg-2.1.jar [new file with mode: 0644] blob
j11lib/jhall.jar [new file with mode: 0644] blob
j11lib/json_simple-1.1.jar [new file with mode: 0644] blob
j11lib/jsoup-1.8.1.jar [new file with mode: 0644] blob
j11lib/jsr311-api-1.1.1.jar [new file with mode: 0644] blob
j11lib/jswingreader-0.3.jar [new file with mode: 0644] blob
j11lib/libquaqua-8.0.jnilib.jar [new file with mode: 0644] blob
j11lib/libquaqua64-8.0.jnilib.jar [new file with mode: 0644] blob
j11lib/log4j-to-slf4j-2.0-rc2.jar [new file with mode: 0644] blob
j11lib/mail-MODULE.jar [new file with mode: 0644] blob
j11lib/miglayout-4.0-swing.jar [new file with mode: 0644] blob
j11lib/mimepull-1.9.11.jar [new file with mode: 0644] blob
j11lib/policy-2.7.6.jar [new file with mode: 0644] blob
j11lib/quaqua-filechooser-only-8.0.jar [new file with mode: 0644] blob
j11lib/regex.jar [new file with mode: 0644] blob
j11lib/saaj-impl.jar [new file with mode: 0644] blob
j11lib/slf4j-api-1.7.26.jar [new file with mode: 0644] blob
j11lib/slf4j-log4j12-1.7.26.jar [new file with mode: 0644] blob
j11lib/stax-ex-1.8.1.jar [new file with mode: 0644] blob
j11lib/stax2-api-4.2.jar [new file with mode: 0644] blob
j11lib/streambuffer-1.5.7.jar [new file with mode: 0644] blob
j11lib/txw2-2.3.2.jar [new file with mode: 0644] blob
j11lib/vamsas-client.jar [new file with mode: 0644] blob
j11lib/wsdl4j-1.6.3.jar [new file with mode: 0644] blob
j11lib/xercesImpl.jar [new file with mode: 0644] blob
j8lib/.cvsignore [new file with mode: 0644] blob
j8lib/JGoogleAnalytics_0.3.jar [new file with mode: 0644] blob
j8lib/Jmol-14.29.17.jar [new file with mode: 0644] blob
j8lib/VARNAv3-93.jar [new file with mode: 0644] blob
j8lib/VAqua5-patch.jar [new file with mode: 0644] blob
j8lib/activation.jar [new file with mode: 0644] blob
j8lib/apache-mime4j-0.6.jar [new file with mode: 0644] blob
j8lib/axis.jar [new file with mode: 0644] blob
j8lib/biojava-core-4.1.0.jar [new file with mode: 0644] blob
j8lib/biojava-ontology-4.1.0.jar [new file with mode: 0644] blob
j8lib/commons-codec-1.3.jar [new file with mode: 0644] blob
j8lib/commons-discovery.jar [new file with mode: 0644] blob
j8lib/commons-logging-1.1.1.jar [new file with mode: 0644] blob
j8lib/groovy-all-2.4.12-indy.jar [new file with mode: 0644] blob
j8lib/htsjdk-2.12.0.jar [new file with mode: 0644] blob
j8lib/httpclient-4.0.3.jar [new file with mode: 0644] blob
j8lib/httpcore-4.0.1.jar [new file with mode: 0644] blob
j8lib/httpmime-4.0.3.jar [new file with mode: 0644] blob
j8lib/intervalstore-v1.1.jar [new file with mode: 0644] blob
j8lib/jabaws-min-client-2.2.0.jar [new file with mode: 0644] blob
j8lib/java-json.jar [new file with mode: 0644] blob
j8lib/jaxrpc.jar [new file with mode: 0644] blob
j8lib/jersey-client-1.19.jar [new file with mode: 0644] blob
j8lib/jersey-core-1.19.jar [new file with mode: 0644] blob
j8lib/jersey-json-1.19.jar [new file with mode: 0644] blob
j8lib/jetty-http-9.2.10.v20150310.jar [new file with mode: 0644] blob
j8lib/jetty-io-9.2.10.v20150310.jar [new file with mode: 0644] blob
j8lib/jetty-server-9.2.10.v20150310.jar [new file with mode: 0644] blob
j8lib/jetty-util-9.2.10.v20150310.jar [new file with mode: 0644] blob
j8lib/jfreesvg-2.1.jar [new file with mode: 0644] blob
j8lib/jhall.jar [new file with mode: 0644] blob
j8lib/json_simple-1.1.jar [new file with mode: 0644] blob
j8lib/jsoup-1.8.1.jar [new file with mode: 0644] blob
j8lib/jsr311-api-1.1.1.jar [new file with mode: 0644] blob
j8lib/jswingreader-0.3.jar [new file with mode: 0644] blob
j8lib/libquaqua-8.0.jnilib.jar [new file with mode: 0644] blob
j8lib/libquaqua64-8.0.jnilib.jar [new file with mode: 0644] blob
j8lib/log4j-to-slf4j-2.0-rc2.jar [new file with mode: 0644] blob
j8lib/mail.jar [new file with mode: 0644] blob
j8lib/miglayout-4.0-swing.jar [new file with mode: 0644] blob
j8lib/quaqua-filechooser-only-8.0.jar [new file with mode: 0644] blob
j8lib/regex.jar [new file with mode: 0644] blob
j8lib/saaj.jar [new file with mode: 0644] blob
j8lib/servlet-api-3.1.jar [new file with mode: 0644] blob
j8lib/slf4j-api-1.7.7.jar [new file with mode: 0644] blob
j8lib/slf4j-log4j12-1.7.7.jar [new file with mode: 0644] blob
j8lib/vamsas-client.jar [new file with mode: 0644] blob
j8lib/wsdl4j.jar [new file with mode: 0644] blob
j8lib/xercesImpl.jar [new file with mode: 0644] blob
j8lib/xml-apis.jar [new file with mode: 0644] blob
lib/FastInfoset.jar [new file with mode: 0644] blob
lib/Jmol-14.29.17-no_netscape.jar [new file with mode: 0644] blob
lib/commons-compress-1.18.jar [new file with mode: 0644] blob
lib/getdown-core.jar [new file with mode: 0644] blob
lib/gmbal-api-only-MODULE.jar [new file with mode: 0644] blob
lib/groovy-2.5.7.jar [new file with mode: 0644] blob
lib/intervalstore-v1.0.jar [new file with mode: 0644] blob
lib/istack-commons-runtime.jar [new file with mode: 0644] blob
lib/javax.activation-api-1.2.0.jar [new file with mode: 0644] blob
lib/javax.annotation-api-1.3.2.jar [new file with mode: 0644] blob
lib/javax.jws-api-1.1.jar [new file with mode: 0644] blob
lib/javax.servlet-api-4.0.1.jar [new file with mode: 0644] blob
lib/javax.xml.rpc-api-1.1.2.jar [new file with mode: 0644] blob
lib/javax.xml.soap-api-1.4.0.jar [new file with mode: 0644] blob
lib/jaxb-api-2.3.1.jar [new file with mode: 0644] blob
lib/jaxb-runtime-2.3.2.jar [new file with mode: 0644] blob
lib/jaxws-api-2.3.1.jar [new file with mode: 0644] blob
lib/jaxws-rt-java9.jar [new file with mode: 0644] blob
lib/jersey-client-1.19.4.jar [new file with mode: 0644] blob
lib/jersey-core-1.19.4.jar [new file with mode: 0644] blob
lib/jersey-json-1.19.4.jar [new file with mode: 0644] blob
lib/mail-MODULE.jar [new file with mode: 0644] blob
lib/mimepull-1.9.11.jar [new file with mode: 0644] blob
lib/policy-2.7.6.jar [new file with mode: 0644] blob
lib/saaj-impl.jar [new file with mode: 0644] blob
lib/slf4j-api-1.7.26.jar [new file with mode: 0644] blob
lib/slf4j-log4j12-1.7.26.jar [new file with mode: 0644] blob
lib/stax-ex-1.8.1.jar [new file with mode: 0644] blob
lib/stax2-api-4.2.jar [new file with mode: 0644] blob
lib/streambuffer-1.5.7.jar [new file with mode: 0644] blob
lib/txw2-2.3.2.jar [new file with mode: 0644] blob
lib/wsdl4j-1.6.3.jar [new file with mode: 0644] blob
libjs/MiGLayout-site.zip diff | blob | history
libjs/VARNA-site.zip diff | blob | history
libjs/intervalstore-site.zip diff | blob | history
methodsDeclared.csv [new file with mode: 0644] blob
src2/fr/README_SWINGJS.txt [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/README_SWINGJS.txt [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/VARNA.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/VARNAPanel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/AlignmentDemo.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/BasicINI.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/FileNameExtensionFilter.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/NussinovDemo.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/NussinovDesignDemo.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/SecStrConsensus.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/SuperpositionDemo.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/VARNAConsoleDemo.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/VARNAEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/VARNAGUI.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/VARNAOnlineDemo.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/VARNAPrinter.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/VARNAcmd.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqAnnotationDataModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqCellEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqCellRenderer.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqFileModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqGUI.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqNode.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqRNASecStrModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqTree.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/FragSeqTreeModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/fragseq/Watcher.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUI.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUICellEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUIRenderer.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITree.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/VARNAGUITreeModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/newGUI/Watcher.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/Connection.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/Couple.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/GraphicalTemplateElement.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/Helix.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/MouseControler.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/TemplateEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/TemplateEditorPanelUI.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/TemplateEdits.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/TemplatePanel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/applications/templateEditor/UnpairedRegion.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/ActionEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/ActionRenderer.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/AnnotationTableModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/BaseSpecialColorEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/BaseTableModel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/ColorRenderer.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/GradientEditorPanel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/ReorderableJList.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/VARNAConsole.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/components/ZoomWindow.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurBPHeightIncrement.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurBaseSpecialColorEditor.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurBlinkingThread.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurBorder.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurClicMovement.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurDemoTextField.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurDraggedMolette.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurGlobalRescale.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurGlobalRotation.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurInterpolator.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurJCheckBoxMenuItem.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurMenu.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurMolette.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurNumPeriod.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurScriptParser.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurSelectionHighlight.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurSliderLabel.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurSpaceBetweenBases.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurTableAnnotations.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurVARNAPanelKeys.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurVueAnnotation.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/controlers/ControleurZoom.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionDrawingAlgorithm.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionEdgeEndpointAlreadyConnected.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionExportFailed.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionInvalidRNATemplate.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionJPEGEncoding.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionLoadingFailed.java [new file with mode: 0644] blob
src2/fr/orsay/lri/varna/exceptions/ExceptionModeleStyleBaseSyntaxError.java [new file with mode: 0644] blob
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