From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 8 Aug 2019 11:38:38 +0000 (+0100)
Subject: JAL-3210 ben testing
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f7be934a51a973c99157ffc318e9d815998d9b45;p=jalview.git

JAL-3210 ben testing
---

diff --git a/.classpath b/.classpath
index 430d9e6..462a76f 100644
--- a/.classpath
+++ b/.classpath
@@ -1,134 +1,133 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" output="bin/main" path="src">
+	<classpathentry kind="output" path="bin/default"/>
+	<classpathentry output="bin/main" kind="src" path="src">
 		<attributes>
 			<attribute name="gradle_scope" value="main"/>
 			<attribute name="gradle_used_by_scope" value=""/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="bin/test" path="test">
+	<classpathentry output="bin/test" kind="src" path="test">
 		<attributes>
-			<attribute name="test" value="true"/>
 			<attribute name="gradle_scope" value="test"/>
 			<attribute name="gradle_used_by_scope" value=""/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
-		<attributes>
-			<attribute name="module" value="true"/>
-		</attributes>
-	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
+	<classpathentry kind="output" path="bin/main"/>
 	<classpathentry kind="lib" path="help"/>
 	<classpathentry kind="lib" path="resources"/>
-	<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-2.5.6.jar"/>
-	<classpathentry kind="lib" path="j11lib/groovy-console-2.5.6.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/i4jruntime.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-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.annotation-api-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
 	<classpathentry kind="lib" path="j11lib/javax.servlet-api-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
+	<classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/regex.jar"/>
+	<classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
+	<classpathentry kind="lib" path="j11lib/policy.jar"/>
 	<classpathentry kind="lib" path="j11lib/jaxb-api-java9.jar"/>
+	<classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.activation-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/i4jruntime.jar"/>
+	<classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
+	<classpathentry kind="lib" path="j11lib/txw2.jar"/>
+	<classpathentry kind="lib" path="j11lib/jersey-json-1.19.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-2.5.6.jar"/>
+	<classpathentry kind="lib" path="j11lib/Jmol-14.29.17-no_netscape.jar"/>
 	<classpathentry kind="lib" path="j11lib/jaxb-runtime.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
+	<classpathentry kind="lib" path="j11lib/slf4j-api-1.7.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
 	<classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
-	<classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
+	<classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
+	<classpathentry kind="lib" path="j11lib/stax-ex.jar"/>
+	<classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/libquaqua64-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
 	<classpathentry kind="lib" path="j11lib/jersey-client-1.19.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/jersey-core-1.19.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/jersey-json-1.19.1.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/intervalstore-v1.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-console-2.5.6.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
+	<classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
+	<classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
+	<classpathentry kind="lib" path="j11lib/jersey-core-1.19.1.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/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/xercesImpl.jar"/>
+	<classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
+	<classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.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.jar"/>
-	<classpathentry kind="lib" path="j11lib/policy.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-1.7.7.jar"/>
-	<classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.7.jar"/>
-	<classpathentry kind="lib" path="j11lib/stax-ex.jar"/>
+	<classpathentry kind="lib" path="j11lib/wsdl4j-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jhall.jar"/>
 	<classpathentry kind="lib" path="j11lib/stax2-api-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/axis.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.annotation-api-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/java-json.jar"/>
+	<classpathentry kind="lib" path="j11lib/mimepull.jar"/>
+	<classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
 	<classpathentry kind="lib" path="j11lib/streambuffer.jar"/>
-	<classpathentry kind="lib" path="j11lib/txw2.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-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/xercesImpl.jar"/>
-	<classpathentry kind="lib" path="utils/ant-contrib-1.0b3.jar">
+	<classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
+	<classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
+	<classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/axis-ant.jar">
+	<classpathentry kind="lib" path="utils/junit-4.12.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/classgraph-4.1.6.jar">
+	<classpathentry kind="lib" path="utils/wsdl4j.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/hamcrest-core-1.3.jar">
+	<classpathentry kind="lib" path="utils/axis-ant.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/jhall.jar">
+	<classpathentry kind="lib" path="utils/classgraph-4.1.6.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/jhindexer.jar">
+	<classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/junit-4.12.jar">
+	<classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
+	<classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/roxes-ant-tasks-1.2-2004-01-30.jar">
+	<classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
@@ -138,7 +137,7 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
+	<classpathentry kind="lib" path="utils/testnglibs/testng.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
@@ -148,36 +147,34 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
+	<classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
+	<classpathentry kind="lib" path="utils/jhindexer.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
+	<classpathentry kind="lib" path="utils/ant-contrib-1.0b3.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar">
+	<classpathentry kind="lib" path="utils/hamcrest-core-1.3.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/testnglibs/testng.jar">
+	<classpathentry kind="lib" path="utils/roxes-ant-tasks-1.2-2004-01-30.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="utils/wsdl4j.jar">
+	<classpathentry kind="lib" path="utils/jhall.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
-	<classpathentry kind="output" path="bin/main"/>
 </classpath>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index 604d902..bc894d5 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -1,298 +1,299 @@
-eclipse.preferences.version=1
-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.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.8
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.release=disabled
-org.eclipse.jdt.core.compiler.source=1.8
-org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=16
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation=16
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16
-org.eclipse.jdt.core.formatter.alignment_for_assignment=0
-org.eclipse.jdt.core.formatter.alignment_for_binary_expression=16
-org.eclipse.jdt.core.formatter.alignment_for_compact_if=16
-org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
-org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16
-org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16
-org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
-org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
-org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
-org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
-org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
-org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
+#
+#Thu Aug 08 12:00:23 BST 2019
+org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert
+org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters=insert
+org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
 org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
-org.eclipse.jdt.core.formatter.blank_lines_after_package=1
-org.eclipse.jdt.core.formatter.blank_lines_before_field=1
-org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration=0
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert
+org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
+org.eclipse.jdt.core.formatter.indentation.size=8
+org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert
+org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off
+org.eclipse.jdt.core.formatter.continuation_indentation=4
 org.eclipse.jdt.core.formatter.blank_lines_before_imports=1
-org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1
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-org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1
-org.eclipse.jdt.core.formatter.blank_lines_before_package=0
-org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1
+org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16
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+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16
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 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
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+org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert
+org.eclipse.jdt.core.formatter.comment.format_html=true
+org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters=insert
+org.eclipse.jdt.core.formatter.alignment_for_compact_if=16
+org.eclipse.jdt.core.formatter.indent_empty_lines=false
+eclipse.preferences.version=1
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
 org.eclipse.jdt.core.formatter.insert_space_after_unary_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert
+org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=true
+org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
+org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=insert
 org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator=insert
-org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_binary_operator=insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1
+org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true
+org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer=insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_cast=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_try=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert=insert
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement=do not insert
+org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1
+org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference=do not insert
+org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16
+org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert
+org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_try=do not insert
 org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast=do not insert
+org.eclipse.jdt.core.formatter.comment.format_block_comments=false
+org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration=do not insert
+org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
+org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
 org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert
+org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
+org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws=insert
 org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression=do not insert
+org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
+org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments=insert
+org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert
+org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=next_line_on_wrap
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert
+org.eclipse.jdt.core.compiler.compliance=11
+org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert
 org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert
 org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
+org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast=insert
+org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line
+org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=next_line
+org.eclipse.jdt.core.formatter.blank_lines_before_package=0
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
 org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert
-org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert
-org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert
-org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert
-org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true
+org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert
 org.eclipse.jdt.core.formatter.join_lines_in_comments=true
-org.eclipse.jdt.core.formatter.join_wrapped_lines=true
-org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=true
-org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
-org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.lineSplit=76
-org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
-org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
-org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
-org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
-org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
+org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert
+org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
+org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert
 org.eclipse.jdt.core.formatter.tabulation.char=space
-org.eclipse.jdt.core.formatter.tabulation.size=2
-org.eclipse.jdt.core.formatter.use_on_off_tags=true
-org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
-org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
-org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
-org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
+org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
+org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1
+org.eclipse.jdt.core.formatter.lineSplit=76
+org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation=do not insert
+org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert
diff --git a/build.xml b/build.xml
index 775df8d..8d2cd7d 100755
--- a/build.xml
+++ b/build.xml
@@ -128,7 +128,7 @@
     <property name="applet.caller-codebase" value="${applet.codebase}" />
 
     <!-- build directory configuration -->
-    <property name="libDir" value="lib" />
+    <property name="libDir" value="j11lib" />
     <property name="resourceDir" value="resources" />
     <property name="helpDir" value="help" />
     <property name="docDir" value="doc" />
@@ -1024,12 +1024,16 @@
 </target>
 
 <target name="eclipse-install" depends="init,prepare">
-
+<!--
   <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
   <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
   <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
+-->
+  <property name="eclipseTempFile" value="eclipse-jee-2019-06-R-linux-gtk-x86_64.tar.gz"/>
+  <property name="eclipseInstallURL" value="http://ftp.fau.de/eclipse/technology/epp/downloads/release/2019-06/R/eclipse-jee-2019-06-R-linux-gtk-x86_64.tar.gz"/>
+  <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/raw/master/sources/net.sf.j2s.core/dist/swingjs/net.sf.j2s.core.jar"/>
 
-  <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
+  <get src="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
   <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
 
   <!-- not needed since we ship transpiler with source
diff --git a/gradle.properties b/gradle.properties
index eec61da..16ff61d 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,7 +1,7 @@
 jalviewDir = .
 
-JAVA_VERSION = 1.8
-#JAVA_VERSION = 11
+#JAVA_VERSION = 1.8
+JAVA_VERSION = 11
 JALVIEW_VERSION = DEVELOPMENT
 INSTALLATION = Source
 jalview_keystore = keys/.keystore
diff --git a/j11lib/Jmol-14.29.17.jar b/j11lib/Jmol-14.29.17-no_netscape.jar
similarity index 67%
rename from j11lib/Jmol-14.29.17.jar
rename to j11lib/Jmol-14.29.17-no_netscape.jar
index 136eb93..a20bcc4 100644
Binary files a/j11lib/Jmol-14.29.17.jar and b/j11lib/Jmol-14.29.17-no_netscape.jar differ
diff --git a/swingjs/net.sf.j2s.core.jar b/swingjs/net.sf.j2s.core.jar
index ec67d8c..54e0f0c 100644
Binary files a/swingjs/net.sf.j2s.core.jar and b/swingjs/net.sf.j2s.core.jar differ
diff --git a/utils/publishHelp.xml b/utils/publishHelp.xml
new file mode 100644
index 0000000..c626a21
--- /dev/null
+++ b/utils/publishHelp.xml
@@ -0,0 +1,64 @@
+<project name="Publish Help Webpages for Jalview" default="pubhtmlhelp">
+
+<target name="pubhtmlhelp">
+  <property name="appletHelpDir" value="../build/distributions/help"/>
+        <!-- finally, publish the help files -->
+        <javac srcdir="." destdir="." includes="help2Website.java"/>
+        <java fork="true" dir="${helpBuildDir}" classpath="." classname="help2Website"/>
+        <delete dir="${appletHelpDir}"/>
+        <copy preservelastmodified="true" overwrite="true" 
+           todir="${appletHelpDir}">
+          <fileset dir="${helpBuildDir}">
+            <include name="*htm*"/>
+            <include name="icons/**.*"/>
+            <include name="html/**/*.*"/>
+            <exclude name="**/CVS"/>
+            <exclude name="CVS"/>
+          </fileset>
+        </copy>
+        <replace dir="${appletHelpDir}">
+        <include name="**/*.htm*"/>
+        <replacetoken><![CDATA[</body>]]></replacetoken>
+        <replacevalue><![CDATA[
+<script type="text/javascript">
+    var gaJsHost = (("https:" == document.location.protocol) ?
+        "https://ssl." : "http://www.");
+    document.write(unescape("%3Cscript src=\'" + gaJsHost +
+        "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try{
+    var pageTracker = _gat._getTracker("'UA-9060947-1'");
+    pageTracker._trackPageview();
+} catch(err) {}
+</script>
+</body>
+]]></replacevalue>
+</replace>
+<echo file="${appletHelpDir}/help.html">
+<![CDATA[<html><head>
+<title>Jalview Documentation</title>
+</head>
+<frameset cols="300,*">
+<frame src="helpTOC.html" name=tocframe scrolling=yes >
+<frame src="html/index.html" name=bodyframe >
+<noframes><body>
+This page requires a browser that supports frames.
+<script type="text/javascript">
+    var gaJsHost = (("https:" == document.location.protocol) ?
+        "https://ssl." : "http://www.");
+    document.write(unescape("%3Cscript src=\'" + gaJsHost +
+        "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+try{
+    var pageTracker = _gat._getTracker("'UA-9060947-1'");
+    pageTracker._trackPageview();
+} catch(err) {}
+</script></body>
+<noframes></frameset>
+</html>
+]]></echo>
+
+  </target>
+</project>