Java 11/Gradle 2.5 upgrade

diff --git a/.classpath b/.classpath
index d3aa906..c9a8e08 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -7,7 +7,7 @@
        <classpathentry kind="lib" path="lib/activation.jar"/>
        <classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
        <classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-       <classpathentry kind="lib" path="lib/jaxrpc.jar"/>
+       <!--  classpathentry kind="lib" path="lib/jaxrpc.jar"/>  -->
        <classpathentry kind="lib" path="lib/jhall.jar"/>
        <classpathentry kind="lib" path="lib/mail.jar"/>
        <classpathentry kind="lib" path="lib/regex.jar"/>
@@ -33,41 +33,109 @@
                        <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
                </attributes>
        </classpathentry>
-       <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
-       <classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
-       <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-       <classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
-       <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
-       <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
-       <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
-       <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
-       <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
-       <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
-       <classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
        <classpathentry kind="lib" path="utils/classgraph-4.1.6.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
-       <classpathentry kind="lib" path="lib/xml-apis.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-server-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/servlet-api-3.1.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-util-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/java-json.jar"/>
-       <classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
-       <classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
-       <classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
-       <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+       <classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
+       <classpathentry kind="lib" path="j11lib/axis.jar"/>
+       <classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
+       <classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
+       <classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
+       <classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
+       <classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
+       <classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-ant-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-bsf-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-cli-commons-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-cli-picocli-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-console-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-datetime-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-dateutil-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-docgenerator-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-groovydoc-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-groovysh-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-jaxb-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-jmx-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-json-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-json-direct-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-jsr223-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-macro-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-nio-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-servlet-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-sql-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-swing-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-templates-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-test-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-test-junit5-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-testng-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/groovy-xml-2.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
+       <classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
+       <!--  classpathentry kind="lib" path="j11lib/intervalstore-v1.0.jar"/>   -->
+       <classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
+       <classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/java-json.jar"/>
+       <classpathentry kind="lib" path="j11lib/javax.activation-api-1.2.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/javax.annotation-api-1.3.2.jar"/>
+       <classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/javax.servlet-api-4.0.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
+       <classpathentry kind="lib" path="j11lib/javax.xml.soap-api-1.4.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/jaxb-api-2.3.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/jaxb-runtime-2.3.2.jar"/>
+       <classpathentry kind="lib" path="j11lib/jaxws-api-2.3.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
+       <classpathentry kind="lib" path="j11lib/jersey-client-1.19.4.jar"/>
+       <classpathentry kind="lib" path="j11lib/jersey-core-1.19.4.jar"/>
+       <classpathentry kind="lib" path="j11lib/jersey-json-1.19.4.jar"/>
+       <classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
+       <classpathentry kind="lib" path="j11lib/jetty-io-9.2.10.v20150310.jar"/>
+       <classpathentry kind="lib" path="j11lib/jetty-server-9.2.10.v20150310.jar"/>
+       <classpathentry kind="lib" path="j11lib/jetty-util-9.2.10.v20150310.jar"/>
+       <classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
+       <classpathentry kind="lib" path="j11lib/jhall.jar"/>
+       <classpathentry kind="lib" path="j11lib/Jmol-14.29.17-no_netscape.jar"/>
+       <classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
+       <classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
+       <classpathentry kind="lib" path="j11lib/libquaqua64-8.0.jnilib.jar"/>
+       <classpathentry kind="lib" path="j11lib/log4j-to-slf4j-2.0-rc2.jar"/>
+       <classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
+       <classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
+       <classpathentry kind="lib" path="j11lib/mimepull-1.9.11.jar"/>
+       <classpathentry kind="lib" path="j11lib/policy-2.7.6.jar"/>
+       <classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
+       <classpathentry kind="lib" path="j11lib/regex.jar"/>
+       <classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
+       <classpathentry kind="lib" path="j11lib/slf4j-api-1.7.26.jar"/>
+       <classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.26.jar"/>
+       <classpathentry kind="lib" path="j11lib/stax-ex-1.8.1.jar"/>
+       <classpathentry kind="lib" path="j11lib/stax2-api-4.2.jar"/>
+       <classpathentry kind="lib" path="j11lib/streambuffer-1.5.7.jar"/>
+       <classpathentry kind="lib" path="j11lib/txw2-2.3.2.jar"/>
+       <classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
+       <classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
+       <classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
+       <classpathentry kind="lib" path="j11lib/wsdl4j-1.6.3.jar"/>
+       <classpathentry kind="lib" path="j11lib/xercesImpl.jar"/>
+       <!-- classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/    -->
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
+               <attributes>
+                       <attribute name="module" value="true"/>
+               </attributes>
+       </classpathentry>
        <classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
-       <classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
        <classpathentry kind="lib" path="utils/testnglibs/bsh-2.0b4.jar"/>
        <classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar"/>
        <classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar"/>

diff --git a/.j2s b/.j2s
index 61231e7..ea8e54f 100644 (file)
--- 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 (file)
--- 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 (file)
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 (file)
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 (file)
index 0000000..5e7d573
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diff --git a/j11lib/VARNAv3-93.jar b/j11lib/VARNAv3-93.jar
new file mode 100644 (file)
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 (file)
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 (file)
index 0000000..1d2282c
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diff --git a/j11lib/axis.jar b/j11lib/axis.jar
new file mode 100644 (file)
index 0000000..90bb798
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diff --git a/j11lib/biojava-core-4.1.0.jar b/j11lib/biojava-core-4.1.0.jar
new file mode 100644 (file)
index 0000000..5a09c1f
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diff --git a/j11lib/biojava-ontology-4.1.0.jar b/j11lib/biojava-ontology-4.1.0.jar
new file mode 100644 (file)
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 (file)
index 0000000..957b675
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diff --git a/j11lib/commons-compress-1.18.jar b/j11lib/commons-compress-1.18.jar
new file mode 100644 (file)
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 (file)
index 0000000..b885548
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diff --git a/j11lib/commons-logging-1.1.1.jar b/j11lib/commons-logging-1.1.1.jar
new file mode 100644 (file)
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 (file)
index 0000000..bbe1476
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diff --git a/j11lib/gmbal-api-only-MODULE.jar b/j11lib/gmbal-api-only-MODULE.jar
new file mode 100644 (file)
index 0000000..06a5fcc
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diff --git a/j11lib/groovy-2.5.7.jar b/j11lib/groovy-2.5.7.jar
new file mode 100644 (file)
index 0000000..e391e93
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diff --git a/j11lib/groovy-ant-2.5.7.jar b/j11lib/groovy-ant-2.5.7.jar
new file mode 100644 (file)
index 0000000..155ec4c
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diff --git a/j11lib/groovy-bsf-2.5.7.jar b/j11lib/groovy-bsf-2.5.7.jar
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index 0000000..3074e3f
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diff --git a/j11lib/groovy-cli-commons-2.5.7.jar b/j11lib/groovy-cli-commons-2.5.7.jar
new file mode 100644 (file)
index 0000000..cf54453
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diff --git a/j11lib/groovy-cli-picocli-2.5.7.jar b/j11lib/groovy-cli-picocli-2.5.7.jar
new file mode 100644 (file)
index 0000000..a05c3e4
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diff --git a/j11lib/groovy-console-2.5.7.jar b/j11lib/groovy-console-2.5.7.jar
new file mode 100644 (file)
index 0000000..d91ca64
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diff --git a/j11lib/groovy-datetime-2.5.7.jar b/j11lib/groovy-datetime-2.5.7.jar
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index 0000000..55aa44b
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diff --git a/j11lib/groovy-dateutil-2.5.7.jar b/j11lib/groovy-dateutil-2.5.7.jar
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index 0000000..ccbddf1
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diff --git a/j11lib/groovy-docgenerator-2.5.7.jar b/j11lib/groovy-docgenerator-2.5.7.jar
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diff --git a/j11lib/groovy-groovydoc-2.5.7.jar b/j11lib/groovy-groovydoc-2.5.7.jar
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diff --git a/j11lib/groovy-groovysh-2.5.7.jar b/j11lib/groovy-groovysh-2.5.7.jar
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diff --git a/j11lib/groovy-jaxb-2.5.7.jar b/j11lib/groovy-jaxb-2.5.7.jar
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diff --git a/j11lib/groovy-jmx-2.5.7.jar b/j11lib/groovy-jmx-2.5.7.jar
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diff --git a/j11lib/groovy-json-2.5.7.jar b/j11lib/groovy-json-2.5.7.jar
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index 0000000..b65d2bb
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diff --git a/j11lib/groovy-json-direct-2.5.7.jar b/j11lib/groovy-json-direct-2.5.7.jar
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diff --git a/j11lib/txw2-2.3.2.jar b/j11lib/txw2-2.3.2.jar
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diff --git a/j11lib/vamsas-client.jar b/j11lib/vamsas-client.jar
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diff --git a/j11lib/wsdl4j-1.6.3.jar b/j11lib/wsdl4j-1.6.3.jar
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diff --git a/j11lib/xercesImpl.jar b/j11lib/xercesImpl.jar
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diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java
index 6f69f8a..0bfc930 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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);