From: BobHanson Date: Wed, 18 Mar 2020 17:59:23 +0000 (-0500) Subject: Java 11/Gradle 2.5 upgrade X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=339f0fa82eabd8c2c97be2833f40f65563987cf1;p=jalview.git Java 11/Gradle 2.5 upgrade --- diff --git a/.classpath b/.classpath index d3aa906..c9a8e08 100644 --- a/.classpath +++ b/.classpath @@ -7,7 +7,7 @@ - + @@ -33,41 +33,109 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - diff --git a/.j2s b/.j2s index 61231e7..ea8e54f 100644 --- a/.j2s +++ b/.j2s @@ -1,4 +1,5 @@ j2s.compiler.status=enable +j2s.compiler.java.version=11 #a semicolon-separated list of package-level file paths to be excluded j2s.excluded.paths=test;testng;utils diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs index 32ad05c..09eecf3 100644 --- a/.settings/org.eclipse.jdt.core.prefs +++ b/.settings/org.eclipse.jdt.core.prefs @@ -10,9 +10,9 @@ org.eclipse.jdt.core.compiler.annotation.nullable.secondary= org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=11 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve -org.eclipse.jdt.core.compiler.compliance=1.8 +org.eclipse.jdt.core.compiler.compliance=11 org.eclipse.jdt.core.compiler.debug.lineNumber=generate org.eclipse.jdt.core.compiler.debug.localVariable=generate org.eclipse.jdt.core.compiler.debug.sourceFile=generate @@ -26,6 +26,7 @@ org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled org.eclipse.jdt.core.compiler.problem.discouragedReference=warning org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore +org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled org.eclipse.jdt.core.compiler.problem.enumIdentifier=error org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore @@ -71,6 +72,7 @@ org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=igno org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore +org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled @@ -104,7 +106,7 @@ org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning org.eclipse.jdt.core.compiler.release=disabled -org.eclipse.jdt.core.compiler.source=1.8 +org.eclipse.jdt.core.compiler.source=11 org.eclipse.jdt.core.formatter.align_assignment_statements_on_columns=false org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false diff --git a/j11lib/FastInfoset.jar b/j11lib/FastInfoset.jar new file mode 100644 index 0000000..2671209 Binary files /dev/null and b/j11lib/FastInfoset.jar differ diff --git a/j11lib/JGoogleAnalytics_0.3.jar b/j11lib/JGoogleAnalytics_0.3.jar new file mode 100644 index 0000000..0dbc98c Binary files /dev/null and b/j11lib/JGoogleAnalytics_0.3.jar differ diff --git a/j11lib/Jmol-14.29.17-no_netscape.jar b/j11lib/Jmol-14.29.17-no_netscape.jar new file mode 100644 index 0000000..5e7d573 Binary files /dev/null and b/j11lib/Jmol-14.29.17-no_netscape.jar differ diff --git a/j11lib/VARNAv3-93.jar b/j11lib/VARNAv3-93.jar new file mode 100644 index 0000000..9d41f6b Binary files /dev/null and b/j11lib/VARNAv3-93.jar differ diff --git a/j11lib/VAqua5-patch.jar b/j11lib/VAqua5-patch.jar new file mode 100644 index 0000000..7b5c27b Binary files /dev/null and b/j11lib/VAqua5-patch.jar differ diff --git a/j11lib/apache-mime4j-0.6.jar b/j11lib/apache-mime4j-0.6.jar new file mode 100644 index 0000000..1d2282c Binary files /dev/null and b/j11lib/apache-mime4j-0.6.jar differ diff --git a/j11lib/axis.jar b/j11lib/axis.jar new file mode 100644 index 0000000..90bb798 Binary files /dev/null and b/j11lib/axis.jar differ diff --git a/j11lib/biojava-core-4.1.0.jar b/j11lib/biojava-core-4.1.0.jar new file mode 100644 index 0000000..5a09c1f Binary files /dev/null and b/j11lib/biojava-core-4.1.0.jar differ diff --git a/j11lib/biojava-ontology-4.1.0.jar b/j11lib/biojava-ontology-4.1.0.jar new file mode 100644 index 0000000..80737d5 Binary files /dev/null and b/j11lib/biojava-ontology-4.1.0.jar differ diff --git a/j11lib/commons-codec-1.3.jar b/j11lib/commons-codec-1.3.jar new file mode 100644 index 0000000..957b675 Binary files /dev/null and b/j11lib/commons-codec-1.3.jar differ diff --git a/j11lib/commons-compress-1.18.jar b/j11lib/commons-compress-1.18.jar new file mode 100644 index 0000000..e401046 Binary files /dev/null and b/j11lib/commons-compress-1.18.jar differ diff --git a/j11lib/commons-discovery.jar b/j11lib/commons-discovery.jar new file mode 100644 index 0000000..b885548 Binary files /dev/null and b/j11lib/commons-discovery.jar differ diff --git a/j11lib/commons-logging-1.1.1.jar b/j11lib/commons-logging-1.1.1.jar new file mode 100644 index 0000000..1deef14 Binary files /dev/null and b/j11lib/commons-logging-1.1.1.jar differ diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar new file mode 100644 index 0000000..bbe1476 Binary files /dev/null and b/j11lib/getdown-core.jar differ diff --git a/j11lib/gmbal-api-only-MODULE.jar b/j11lib/gmbal-api-only-MODULE.jar new file mode 100644 index 0000000..06a5fcc Binary files /dev/null and b/j11lib/gmbal-api-only-MODULE.jar differ diff --git a/j11lib/groovy-2.5.7.jar b/j11lib/groovy-2.5.7.jar new file mode 100644 index 0000000..e391e93 Binary files /dev/null and b/j11lib/groovy-2.5.7.jar differ diff --git a/j11lib/groovy-ant-2.5.7.jar b/j11lib/groovy-ant-2.5.7.jar new file mode 100644 index 0000000..155ec4c Binary files /dev/null and b/j11lib/groovy-ant-2.5.7.jar differ diff --git a/j11lib/groovy-bsf-2.5.7.jar b/j11lib/groovy-bsf-2.5.7.jar new file mode 100644 index 0000000..3074e3f Binary files /dev/null and b/j11lib/groovy-bsf-2.5.7.jar differ diff --git a/j11lib/groovy-cli-commons-2.5.7.jar b/j11lib/groovy-cli-commons-2.5.7.jar new file mode 100644 index 0000000..cf54453 Binary files /dev/null and b/j11lib/groovy-cli-commons-2.5.7.jar differ diff --git a/j11lib/groovy-cli-picocli-2.5.7.jar b/j11lib/groovy-cli-picocli-2.5.7.jar new file mode 100644 index 0000000..a05c3e4 Binary files /dev/null and b/j11lib/groovy-cli-picocli-2.5.7.jar differ diff --git a/j11lib/groovy-console-2.5.7.jar b/j11lib/groovy-console-2.5.7.jar new file mode 100644 index 0000000..d91ca64 Binary files /dev/null and b/j11lib/groovy-console-2.5.7.jar differ diff --git a/j11lib/groovy-datetime-2.5.7.jar b/j11lib/groovy-datetime-2.5.7.jar new file mode 100644 index 0000000..55aa44b Binary files /dev/null and b/j11lib/groovy-datetime-2.5.7.jar differ diff --git a/j11lib/groovy-dateutil-2.5.7.jar b/j11lib/groovy-dateutil-2.5.7.jar new file mode 100644 index 0000000..ccbddf1 Binary files /dev/null and b/j11lib/groovy-dateutil-2.5.7.jar differ diff --git a/j11lib/groovy-docgenerator-2.5.7.jar b/j11lib/groovy-docgenerator-2.5.7.jar new file mode 100644 index 0000000..a895272 Binary files /dev/null and b/j11lib/groovy-docgenerator-2.5.7.jar differ diff --git a/j11lib/groovy-groovydoc-2.5.7.jar b/j11lib/groovy-groovydoc-2.5.7.jar new file mode 100644 index 0000000..8917544 Binary files /dev/null and b/j11lib/groovy-groovydoc-2.5.7.jar differ diff --git a/j11lib/groovy-groovysh-2.5.7.jar b/j11lib/groovy-groovysh-2.5.7.jar new file mode 100644 index 0000000..2683ab1 Binary files /dev/null and b/j11lib/groovy-groovysh-2.5.7.jar differ diff --git a/j11lib/groovy-jaxb-2.5.7.jar b/j11lib/groovy-jaxb-2.5.7.jar new file mode 100644 index 0000000..879ffb4 Binary files /dev/null and b/j11lib/groovy-jaxb-2.5.7.jar differ diff --git a/j11lib/groovy-jmx-2.5.7.jar b/j11lib/groovy-jmx-2.5.7.jar new file mode 100644 index 0000000..5d8e104 Binary files /dev/null and b/j11lib/groovy-jmx-2.5.7.jar differ diff --git a/j11lib/groovy-json-2.5.7.jar b/j11lib/groovy-json-2.5.7.jar new file mode 100644 index 0000000..b65d2bb Binary files /dev/null and b/j11lib/groovy-json-2.5.7.jar differ diff --git a/j11lib/groovy-json-direct-2.5.7.jar b/j11lib/groovy-json-direct-2.5.7.jar new file mode 100644 index 0000000..2f16d68 Binary files /dev/null and b/j11lib/groovy-json-direct-2.5.7.jar differ diff --git a/j11lib/groovy-jsr223-2.5.7.jar b/j11lib/groovy-jsr223-2.5.7.jar new file mode 100644 index 0000000..ff4c7db Binary files /dev/null and b/j11lib/groovy-jsr223-2.5.7.jar differ diff --git a/j11lib/groovy-macro-2.5.7.jar b/j11lib/groovy-macro-2.5.7.jar new file mode 100644 index 0000000..accf49e Binary files /dev/null and b/j11lib/groovy-macro-2.5.7.jar differ diff --git a/j11lib/groovy-nio-2.5.7.jar b/j11lib/groovy-nio-2.5.7.jar new file mode 100644 index 0000000..0273f0c Binary files /dev/null and b/j11lib/groovy-nio-2.5.7.jar differ diff --git a/j11lib/groovy-servlet-2.5.7.jar b/j11lib/groovy-servlet-2.5.7.jar new file mode 100644 index 0000000..6145239 Binary files /dev/null and b/j11lib/groovy-servlet-2.5.7.jar differ diff --git a/j11lib/groovy-sql-2.5.7.jar b/j11lib/groovy-sql-2.5.7.jar new file mode 100644 index 0000000..a76f952 Binary files /dev/null and b/j11lib/groovy-sql-2.5.7.jar differ diff --git a/j11lib/groovy-swing-2.5.7.jar b/j11lib/groovy-swing-2.5.7.jar new file mode 100644 index 0000000..3864019 Binary files /dev/null and b/j11lib/groovy-swing-2.5.7.jar differ diff --git a/j11lib/groovy-templates-2.5.7.jar b/j11lib/groovy-templates-2.5.7.jar new file mode 100644 index 0000000..74d731b Binary files /dev/null and b/j11lib/groovy-templates-2.5.7.jar differ diff --git a/j11lib/groovy-test-2.5.7.jar b/j11lib/groovy-test-2.5.7.jar new file mode 100644 index 0000000..9b79e94 Binary files /dev/null and b/j11lib/groovy-test-2.5.7.jar differ diff --git a/j11lib/groovy-test-junit5-2.5.7.jar b/j11lib/groovy-test-junit5-2.5.7.jar new file mode 100644 index 0000000..95815ff Binary files /dev/null and b/j11lib/groovy-test-junit5-2.5.7.jar differ diff --git a/j11lib/groovy-testng-2.5.7.jar b/j11lib/groovy-testng-2.5.7.jar new file mode 100644 index 0000000..77884fa Binary files /dev/null and b/j11lib/groovy-testng-2.5.7.jar differ diff --git a/j11lib/groovy-xml-2.5.7.jar b/j11lib/groovy-xml-2.5.7.jar new file mode 100644 index 0000000..034cdf9 Binary files /dev/null and b/j11lib/groovy-xml-2.5.7.jar differ diff --git a/j11lib/htsjdk-2.12.0.jar b/j11lib/htsjdk-2.12.0.jar new file mode 100644 index 0000000..1df12b2 Binary files /dev/null and b/j11lib/htsjdk-2.12.0.jar differ diff --git a/j11lib/httpclient-4.0.3.jar b/j11lib/httpclient-4.0.3.jar new file mode 100644 index 0000000..fd0d377 Binary files /dev/null and b/j11lib/httpclient-4.0.3.jar differ diff --git a/j11lib/httpcore-4.0.1.jar b/j11lib/httpcore-4.0.1.jar new file mode 100644 index 0000000..4aef35e Binary files /dev/null and b/j11lib/httpcore-4.0.1.jar differ diff --git a/j11lib/httpmime-4.0.3.jar b/j11lib/httpmime-4.0.3.jar new file mode 100644 index 0000000..0dfd331 Binary files /dev/null and b/j11lib/httpmime-4.0.3.jar differ diff --git a/j11lib/istack-commons-runtime.jar b/j11lib/istack-commons-runtime.jar new file mode 100644 index 0000000..2fe5b82 Binary files /dev/null and b/j11lib/istack-commons-runtime.jar differ diff --git a/j11lib/jabaws-min-client-2.2.0.jar b/j11lib/jabaws-min-client-2.2.0.jar new file mode 100644 index 0000000..37426c3 Binary files /dev/null and b/j11lib/jabaws-min-client-2.2.0.jar differ diff --git a/j11lib/java-json.jar b/j11lib/java-json.jar new file mode 100644 index 0000000..2f211e3 Binary files /dev/null and b/j11lib/java-json.jar differ diff --git a/j11lib/javax.activation-api-1.2.0.jar b/j11lib/javax.activation-api-1.2.0.jar new file mode 100644 index 0000000..986c365 Binary files /dev/null and b/j11lib/javax.activation-api-1.2.0.jar differ diff --git a/j11lib/javax.annotation-api-1.3.2.jar b/j11lib/javax.annotation-api-1.3.2.jar new file mode 100644 index 0000000..a8a470a Binary files /dev/null and b/j11lib/javax.annotation-api-1.3.2.jar differ diff --git a/j11lib/javax.jws-api-1.1.jar b/j11lib/javax.jws-api-1.1.jar new file mode 100644 index 0000000..d4c06d2 Binary files /dev/null and b/j11lib/javax.jws-api-1.1.jar differ diff --git a/j11lib/javax.servlet-api-4.0.1.jar b/j11lib/javax.servlet-api-4.0.1.jar new file mode 100644 index 0000000..844ec7f Binary files /dev/null and b/j11lib/javax.servlet-api-4.0.1.jar differ diff --git a/j11lib/javax.xml.rpc-api-1.1.2.jar b/j11lib/javax.xml.rpc-api-1.1.2.jar new file mode 100644 index 0000000..61ac294 Binary files /dev/null and b/j11lib/javax.xml.rpc-api-1.1.2.jar differ diff --git a/j11lib/javax.xml.soap-api-1.4.0.jar b/j11lib/javax.xml.soap-api-1.4.0.jar new file mode 100644 index 0000000..c47a3b0 Binary files /dev/null and b/j11lib/javax.xml.soap-api-1.4.0.jar differ diff --git a/j11lib/jaxb-api-2.3.1.jar b/j11lib/jaxb-api-2.3.1.jar new file mode 100644 index 0000000..4565865 Binary files /dev/null and b/j11lib/jaxb-api-2.3.1.jar differ diff --git a/j11lib/jaxb-runtime-2.3.2.jar b/j11lib/jaxb-runtime-2.3.2.jar new file mode 100644 index 0000000..62f8719 Binary files /dev/null and b/j11lib/jaxb-runtime-2.3.2.jar differ diff --git a/j11lib/jaxws-api-2.3.1.jar b/j11lib/jaxws-api-2.3.1.jar new file mode 100644 index 0000000..806c0e1 Binary files /dev/null and b/j11lib/jaxws-api-2.3.1.jar differ diff --git a/j11lib/jaxws-rt-java9.jar b/j11lib/jaxws-rt-java9.jar new file mode 100644 index 0000000..f380d18 Binary files /dev/null and b/j11lib/jaxws-rt-java9.jar differ diff --git a/j11lib/jersey-client-1.19.4.jar b/j11lib/jersey-client-1.19.4.jar new file mode 100644 index 0000000..0588ee2 Binary files /dev/null and b/j11lib/jersey-client-1.19.4.jar differ diff --git a/j11lib/jersey-core-1.19.4.jar b/j11lib/jersey-core-1.19.4.jar new file mode 100644 index 0000000..e800c60 Binary files /dev/null and b/j11lib/jersey-core-1.19.4.jar differ diff --git a/j11lib/jersey-json-1.19.4.jar b/j11lib/jersey-json-1.19.4.jar new file mode 100644 index 0000000..c79271b Binary files /dev/null and b/j11lib/jersey-json-1.19.4.jar differ diff --git a/j11lib/jetty-http-9.2.10.v20150310.jar b/j11lib/jetty-http-9.2.10.v20150310.jar new file mode 100644 index 0000000..15aff51 Binary files /dev/null and b/j11lib/jetty-http-9.2.10.v20150310.jar differ diff --git a/j11lib/jetty-io-9.2.10.v20150310.jar b/j11lib/jetty-io-9.2.10.v20150310.jar new file mode 100644 index 0000000..56cee2c Binary files /dev/null and b/j11lib/jetty-io-9.2.10.v20150310.jar differ diff --git a/j11lib/jetty-server-9.2.10.v20150310.jar b/j11lib/jetty-server-9.2.10.v20150310.jar new file mode 100644 index 0000000..815cb08 Binary files /dev/null and b/j11lib/jetty-server-9.2.10.v20150310.jar differ diff --git a/j11lib/jetty-util-9.2.10.v20150310.jar b/j11lib/jetty-util-9.2.10.v20150310.jar new file mode 100644 index 0000000..fe27758 Binary files /dev/null and b/j11lib/jetty-util-9.2.10.v20150310.jar differ diff --git a/j11lib/jfreesvg-2.1.jar b/j11lib/jfreesvg-2.1.jar new file mode 100644 index 0000000..91d453c Binary files /dev/null and b/j11lib/jfreesvg-2.1.jar differ diff --git a/j11lib/jhall.jar b/j11lib/jhall.jar new file mode 100644 index 0000000..ff08af0 Binary files /dev/null and b/j11lib/jhall.jar differ diff --git a/j11lib/json_simple-1.1.jar b/j11lib/json_simple-1.1.jar new file mode 100644 index 0000000..f395f41 Binary files /dev/null and b/j11lib/json_simple-1.1.jar differ diff --git a/j11lib/jsoup-1.8.1.jar b/j11lib/jsoup-1.8.1.jar new file mode 100644 index 0000000..ae717d4 Binary files /dev/null and b/j11lib/jsoup-1.8.1.jar differ diff --git a/j11lib/jsr311-api-1.1.1.jar b/j11lib/jsr311-api-1.1.1.jar new file mode 100644 index 0000000..ec8bc81 Binary files /dev/null and b/j11lib/jsr311-api-1.1.1.jar differ diff --git a/j11lib/jswingreader-0.3.jar b/j11lib/jswingreader-0.3.jar new file mode 100644 index 0000000..c632130 Binary files /dev/null and b/j11lib/jswingreader-0.3.jar differ diff --git a/j11lib/libquaqua-8.0.jnilib.jar b/j11lib/libquaqua-8.0.jnilib.jar new file mode 100644 index 0000000..79383b0 Binary files /dev/null and b/j11lib/libquaqua-8.0.jnilib.jar differ diff --git a/j11lib/libquaqua64-8.0.jnilib.jar b/j11lib/libquaqua64-8.0.jnilib.jar new file mode 100644 index 0000000..efb46a4 Binary files /dev/null and b/j11lib/libquaqua64-8.0.jnilib.jar differ diff --git a/j11lib/log4j-to-slf4j-2.0-rc2.jar b/j11lib/log4j-to-slf4j-2.0-rc2.jar new file mode 100644 index 0000000..4bbf54a Binary files /dev/null and b/j11lib/log4j-to-slf4j-2.0-rc2.jar differ diff --git a/j11lib/mail-MODULE.jar b/j11lib/mail-MODULE.jar new file mode 100644 index 0000000..367ca9e Binary files /dev/null and b/j11lib/mail-MODULE.jar differ diff --git a/j11lib/miglayout-4.0-swing.jar b/j11lib/miglayout-4.0-swing.jar new file mode 100644 index 0000000..7b6a22c Binary files /dev/null and b/j11lib/miglayout-4.0-swing.jar differ diff --git a/j11lib/mimepull-1.9.11.jar b/j11lib/mimepull-1.9.11.jar new file mode 100644 index 0000000..99a4aba Binary files /dev/null and b/j11lib/mimepull-1.9.11.jar differ diff --git a/j11lib/policy-2.7.6.jar b/j11lib/policy-2.7.6.jar new file mode 100644 index 0000000..56b0e31 Binary files /dev/null and b/j11lib/policy-2.7.6.jar differ diff --git a/j11lib/quaqua-filechooser-only-8.0.jar b/j11lib/quaqua-filechooser-only-8.0.jar new file mode 100644 index 0000000..182e0da Binary files /dev/null and b/j11lib/quaqua-filechooser-only-8.0.jar differ diff --git a/j11lib/regex.jar b/j11lib/regex.jar new file mode 100644 index 0000000..3e29d22 Binary files /dev/null and b/j11lib/regex.jar differ diff --git a/j11lib/saaj-impl.jar b/j11lib/saaj-impl.jar new file mode 100644 index 0000000..7eda25c Binary files /dev/null and b/j11lib/saaj-impl.jar differ diff --git a/j11lib/slf4j-api-1.7.26.jar b/j11lib/slf4j-api-1.7.26.jar new file mode 100644 index 0000000..d2f27ac Binary files /dev/null and b/j11lib/slf4j-api-1.7.26.jar differ diff --git a/j11lib/slf4j-log4j12-1.7.26.jar b/j11lib/slf4j-log4j12-1.7.26.jar new file mode 100644 index 0000000..aed1195 Binary files /dev/null and b/j11lib/slf4j-log4j12-1.7.26.jar differ diff --git a/j11lib/stax-ex-1.8.1.jar b/j11lib/stax-ex-1.8.1.jar new file mode 100644 index 0000000..a200db5 Binary files /dev/null and b/j11lib/stax-ex-1.8.1.jar differ diff --git a/j11lib/stax2-api-4.2.jar b/j11lib/stax2-api-4.2.jar new file mode 100644 index 0000000..668dd42 Binary files /dev/null and b/j11lib/stax2-api-4.2.jar differ diff --git a/j11lib/streambuffer-1.5.7.jar b/j11lib/streambuffer-1.5.7.jar new file mode 100644 index 0000000..efc9a68 Binary files /dev/null and b/j11lib/streambuffer-1.5.7.jar differ diff --git a/j11lib/txw2-2.3.2.jar b/j11lib/txw2-2.3.2.jar new file mode 100644 index 0000000..0d5ac01 Binary files /dev/null and b/j11lib/txw2-2.3.2.jar differ diff --git a/j11lib/vamsas-client.jar b/j11lib/vamsas-client.jar new file mode 100644 index 0000000..2634954 Binary files /dev/null and b/j11lib/vamsas-client.jar differ diff --git a/j11lib/wsdl4j-1.6.3.jar b/j11lib/wsdl4j-1.6.3.jar new file mode 100644 index 0000000..b9c10b9 Binary files /dev/null and b/j11lib/wsdl4j-1.6.3.jar differ diff --git a/j11lib/xercesImpl.jar b/j11lib/xercesImpl.jar new file mode 100644 index 0000000..0aaa990 Binary files /dev/null and b/j11lib/xercesImpl.jar differ diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java index 6f69f8a..0bfc930 100644 --- a/src/jalview/bin/JalviewJS2.java +++ b/src/jalview/bin/JalviewJS2.java @@ -38,8 +38,8 @@ public class JalviewJS2 "open", "examples/uniref50.fa", "features", "examples/exampleFeatures.txt" - , "noannotation" - , "showoverview" + // , "noannotation" + // , "showoverview" // , "png", "test-bh.png" }; } diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index ddadd6d..341b2a8 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1172,10 +1172,15 @@ public class FeatureSettings extends JPanel */ boolean updateFeatureRenderer(Object[][] data, boolean visibleNew) { + System.out + .println("FeatureSettings.updateFeatureRenderer " + visibleNew); + new NullPointerException("testing").printStackTrace(); FeatureSettingsBean[] rowData = getTableAsBeans(data); if (fr.setFeaturePriority(rowData, visibleNew)) { + System.out.println( + "FeatureSettings.updateFeatureRenderer paintingAlignment"); af.alignPanel.paintAlignment(true, true); return true; } diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 74263b1..051523a 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -208,32 +208,43 @@ public class Discoverer implements Runnable, ApplicationSingletonI jalview.bin.Cache.log.debug("Setting default services"); d.services = new Hashtable<>(); // Muscle, Clustal and JPred. - ServiceHandle[] defServices = { new ServiceHandle("MsaWS", - "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " - + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", - MessageManager.getString( - "label.muscle_multiple_protein_sequence_alignment")), - new ServiceHandle("MsaWS", - "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " - + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" - + " Nucleic Acids Research, 33 511-518", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", - MessageManager.getString( - "label.mafft_multiple_sequence_alignment")), - new ServiceHandle("MsaWS", - "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" - + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." - + " Nucleic Acids Research, 22 4673-4680", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", - MessageManager.getString( - "label.clustalw_multiple_sequence_alignment")), - new ServiceHandle("SecStrPred", - "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server" - + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)" - + "\ndoi://10.1093/nar/gkv332", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", - "JPred Secondary Structure Prediction") }; + ServiceHandle[] defServices = new ServiceHandle[0]; + if (false) + { + try + { + // BH 2020.03.18 issue with applet branch Module problem. + defServices = new ServiceHandle[] { new ServiceHandle("MsaWS", + "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " + + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", + MessageManager.getString( + "label.muscle_multiple_protein_sequence_alignment")), + new ServiceHandle("MsaWS", + "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " + + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" + + " Nucleic Acids Research, 33 511-518", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", + MessageManager.getString( + "label.mafft_multiple_sequence_alignment")), + new ServiceHandle("MsaWS", + "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" + + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." + + " Nucleic Acids Research, 22 4673-4680", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", + MessageManager.getString( + "label.clustalw_multiple_sequence_alignment")), + new ServiceHandle("SecStrPred", + "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server" + + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)" + + "\ndoi://10.1093/nar/gkv332", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", + "JPred Secondary Structure Prediction") }; + } catch (Throwable e) + { + + } + } d.services = new Hashtable<>(); d.serviceList = new Vector<>(); buildServiceLists(defServices, d.serviceList, d.services);