From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 24 May 2019 10:31:34 +0000 (+0100)
Subject: Merge branch 'develop' into trialMerge
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8946f41687f4c822ac8d15ee8551f23f156735c4;p=jalview.git

Merge branch 'develop' into trialMerge

Conflicts:
	.classpath
	.project
	.settings/org.eclipse.jdt.core.prefs
	.settings/org.eclipse.jdt.groovy.core.prefs
	.settings/org.eclipse.jdt.ui.prefs
	build.xml
	src/MCview/AppletPDBCanvas.java
	src/MCview/Atom.java
	src/MCview/PDBCanvas.java
	src/jalview/appletgui/EmbmenuFrame.java
	src/jalview/appletgui/OverviewPanel.java
	src/jalview/appletgui/SeqPanel.java
	src/jalview/bin/Jalview.java
	src/jalview/ext/paradise/Annotate3D.java
	src/jalview/gui/AlignFrame.java
	src/jalview/gui/Desktop.java
	src/jalview/gui/FeatureRenderer.java
	src/jalview/gui/FeatureTypeSettings.java
	src/jalview/io/FileLoader.java
	src/jalview/jbgui/GDesktop.java
	src/jalview/util/ImageMaker.java
	src/jalview/util/Platform.java
---

8946f41687f4c822ac8d15ee8551f23f156735c4
diff --cc .classpath
index 004d432,0000000..430d9e6
mode 100644,000000..100644
--- a/.classpath
+++ b/.classpath
@@@ -1,74 -1,0 +1,183 @@@
 +<?xml version="1.0" encoding="UTF-8"?>
 +<classpath>
- 	<classpathentry kind="src" path="src"/>
- 	<classpathentry kind="src" path="src2"/>
- 	<classpathentry kind="src" path="test"/>
- 	<classpathentry kind="src" path="utils"/>
- 	<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/jhall.jar"/>
- 	<classpathentry kind="lib" path="lib/mail.jar"/>
- 	<classpathentry kind="lib" path="lib/regex.jar"/>
- 	<classpathentry kind="lib" path="lib/saaj.jar"/>
- 	<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
- 	<classpathentry kind="lib" path="lib/xercesImpl.jar"/>
- 	<classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
- 	<classpathentry kind="lib" path="lib/vamsas-client.jar"/>
- 	<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
- 	<classpathentry kind="lib" path="lib/apache-mime4j-0.6.jar" sourcepath="G:/InstallsDir/Sources for Development/apache-mime4j-0.6-src.zip"/>
- 	<classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
- 		<attributes>
- 			<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/httpcore-4.0.1.jar">
- 		<attributes>
- 			<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/httpmime-4.0.3.jar">
- 		<attributes>
- 			<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="con" path="org.testng.TESTNG_CONTAINER"/>
- 	<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 exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
++	<classpathentry kind="src" output="bin/main" 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">
++		<attributes>
++			<attribute name="test" value="true"/>
++			<attribute name="gradle_scope" value="test"/>
++			<attribute name="gradle_used_by_scope" value=""/>
++		</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.buildship.core.gradleclasspathcontainer"/>
++	<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/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/jaxb-api-java9.jar"/>
++	<classpathentry kind="lib" path="j11lib/jaxb-runtime.jar"/>
++	<classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
++	<classpathentry kind="lib" path="j11lib/jaxws-rt-java9.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/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/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/stax2-api-MODULE.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">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/axis-ant.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/classgraph-4.1.6.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/hamcrest-core-1.3.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/jhall.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/jhindexer.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/junit-4.12.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<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/testnglibs/bsh-2.0b4.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/testnglibs/testng.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
++	<classpathentry kind="lib" path="utils/wsdl4j.jar">
++		<attributes>
++			<attribute name="test" value="true"/>
++		</attributes>
++	</classpathentry>
 +	<classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
- 	<classpathentry kind="lib" path="lib/intervalstore-v1.0.jar"/>
- 	<classpathentry kind="output" path="classes"/>
++	<classpathentry kind="output" path="bin/main"/>
 +</classpath>
diff --cc .project
index 6c40472,0000000..d4d0c20
mode 100644,000000..100644
--- a/.project
+++ b/.project
@@@ -1,37 -1,0 +1,23 @@@
 +<?xml version="1.0" encoding="UTF-8"?>
 +<projectDescription>
- 	<name>Jalview Release 2.7-old</name>
++	<name>Jalview with gradle build</name>
 +	<comment></comment>
- 	<projects>
- 	</projects>
++	<projects/>
++	<natures>
++		<nature>org.eclipse.jdt.core.javanature</nature>
++		<nature>org.eclipse.jdt.groovy.core.groovyNature</nature>
++		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
++	</natures>
 +	<buildSpec>
 +		<buildCommand>
 +			<name>org.eclipse.jdt.core.javabuilder</name>
- 			<arguments>
- 			</arguments>
- 		</buildCommand>
- 		<buildCommand>
- 			<name>org.eclipse.wst.common.project.facet.core.builder</name>
- 			<arguments>
- 			</arguments>
++			<arguments/>
 +		</buildCommand>
 +		<buildCommand>
- 			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
- 			<triggers>full,incremental,</triggers>
- 			<arguments>
- 				<dictionary>
- 					<key>LaunchConfigHandle</key>
- 					<value>&lt;project&gt;/.externalToolBuilders/Jalview Release indices [Builder].launch</value>
- 				</dictionary>
- 			</arguments>
++			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
++			<arguments/>
 +		</buildCommand>
 +	</buildSpec>
- 	<natures>
- 		<nature>org.eclipse.jdt.groovy.core.groovyNature</nature>
- 		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
- 		<nature>org.eclipse.jdt.core.javanature</nature>
- 		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
- 		<nature>de.tud.st.ispace.builder.ISpaceNature</nature>
- 		<nature>org.eclipse.jem.beaninfo.BeanInfoNature</nature>
- 	</natures>
++	<linkedResources/>
++	<filteredResources/>
 +</projectDescription>
diff --cc .settings/org.eclipse.jdt.core.prefs
index 32ad05c,0000000..604d902
mode 100644,000000..100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@@ -1,421 -1,0 +1,298 @@@
 +eclipse.preferences.version=1
- org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
- org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
- org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
- org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
- org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
- org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
- org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
- 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.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.annotationSuperInterface=warning
 +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
- org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
- org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
- org.eclipse.jdt.core.compiler.problem.deadCode=warning
- org.eclipse.jdt.core.compiler.problem.deprecation=warning
- 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.enumIdentifier=error
- org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
- org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
- org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
- org.eclipse.jdt.core.compiler.problem.fieldHiding=ignore
- org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
- org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
- org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
- org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
- org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
- org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
- org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
- org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
- org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore
- org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
- org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
- org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
- org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
- org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=ignore
- org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=ignore
- org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
- org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
- org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
- org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
- org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
- org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
- org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
- org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning
- org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
- org.eclipse.jdt.core.compiler.problem.nullReference=warning
- org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
- org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
- org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
- org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
- org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
- org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore
- org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
- org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
- org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
- org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
- org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore
- org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
- 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.specialParameterHidingField=disabled
- org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
- org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
- org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
- org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
- org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=warning
- org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
- org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
- org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
- org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
- org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
- org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
- org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
- org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore
- org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
- org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore
- org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
- org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
- org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
- org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
- org.eclipse.jdt.core.compiler.problem.unusedImport=warning
- org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
- org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
- org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore
- org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore
- org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
- org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
- org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
- org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
- 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.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
- org.eclipse.jdt.core.formatter.align_variable_declarations_on_columns=false
- org.eclipse.jdt.core.formatter.align_with_spaces=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_compact_loops=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_expressions_in_for_loop_header=0
 +org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
- org.eclipse.jdt.core.formatter.alignment_for_module_statements=16
 +org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
- org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0
 +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_type_arguments=0
- org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0
 +org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
 +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.blank_lines_before_imports=1
 +org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1
 +org.eclipse.jdt.core.formatter.blank_lines_before_method=1
 +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.blank_lines_between_type_declarations=1
 +org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=next_line_on_wrap
 +org.eclipse.jdt.core.formatter.brace_position_for_block=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_block_in_case=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line
 +org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_switch=next_line
 +org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line
- org.eclipse.jdt.core.formatter.comment.align_tags_descriptions_grouped=false
- org.eclipse.jdt.core.formatter.comment.align_tags_names_descriptions=false
 +org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
 +org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
- org.eclipse.jdt.core.formatter.comment.count_line_length_from_starting_position=false
 +org.eclipse.jdt.core.formatter.comment.format_block_comments=false
 +org.eclipse.jdt.core.formatter.comment.format_header=false
 +org.eclipse.jdt.core.formatter.comment.format_html=true
 +org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
 +org.eclipse.jdt.core.formatter.comment.format_line_comments=true
 +org.eclipse.jdt.core.formatter.comment.format_source_code=true
 +org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
 +org.eclipse.jdt.core.formatter.comment.indent_root_tags=true
 +org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
 +org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
 +org.eclipse.jdt.core.formatter.comment.line_length=80
 +org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
 +org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
 +org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false
 +org.eclipse.jdt.core.formatter.compact_else_if=true
 +org.eclipse.jdt.core.formatter.continuation_indentation=4
 +org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2
 +org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off
 +org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on
 +org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line=false
 +org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column=true
 +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true
 +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true
 +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true
 +org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header=true
 +org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true
 +org.eclipse.jdt.core.formatter.indent_empty_lines=false
 +org.eclipse.jdt.core.formatter.indent_statements_compare_to_block=true
 +org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
 +org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
 +org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
- org.eclipse.jdt.core.formatter.indentation.size=2
- org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_enum_constant=insert
++org.eclipse.jdt.core.formatter.indentation.size=8
 +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert
 +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_after_type_annotation=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement=do not insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=insert
 +org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_binary_operator=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_case=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_labeled_statement=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments=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.insert_space_after_opening_brace_in_array_initializer=insert
 +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_bracket_in_array_reference=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch=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_after_opening_paren_in_enum_constant=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for=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_after_opening_paren_in_method_declaration=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=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_after_opening_paren_in_while=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard=do not insert
 +org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert
 +org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_try_resources=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_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_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_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_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.insert_space_before_opening_bracket_in_array_allocation_expression=do not 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.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.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_simple_do_while_body_on_same_line=false
- org.eclipse.jdt.core.formatter.keep_simple_for_body_on_same_line=false
- org.eclipse.jdt.core.formatter.keep_simple_while_body_on_same_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.parentheses_positions_in_annotation=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_catch_clause=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines
- org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines
 +org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
 +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_assignment_operator=false
 +org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
- org.eclipse.jdt.core.formatter.wrap_before_conditional_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.javaFormatter=org.eclipse.jdt.core.defaultJavaFormatter
diff --cc src/MCview/AppletPDBCanvas.java
index 0000000,c6553f8..bc36d9e
mode 000000,100644..100644
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@@ -1,0 -1,1264 +1,6 @@@
 -/*
 - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 - * Copyright (C) $$Year-Rel$$ The Jalview Authors
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3
 - * of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License
 - * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 - * The Jalview Authors are detailed in the 'AUTHORS' file.
 - */
+ package MCview;
+ 
 -import jalview.analysis.AlignSeq;
 -import jalview.appletgui.AlignmentPanel;
 -import jalview.appletgui.FeatureRenderer;
 -import jalview.appletgui.SequenceRenderer;
 -import jalview.datamodel.PDBEntry;
 -import jalview.datamodel.SequenceI;
 -import jalview.io.DataSourceType;
 -import jalview.io.StructureFile;
 -import jalview.renderer.seqfeatures.FeatureColourFinder;
 -import jalview.structure.AtomSpec;
 -import jalview.structure.StructureListener;
 -import jalview.structure.StructureMapping;
 -import jalview.structure.StructureSelectionManager;
 -import jalview.util.MessageManager;
 -
 -import java.awt.Color;
 -import java.awt.Dimension;
 -import java.awt.event.InputEvent;import java.awt.Font;
 -import java.awt.Graphics;
 -import java.awt.Image;
 -// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
 -import java.awt.Panel;
 -import java.awt.event.KeyAdapter;
 -import java.awt.event.KeyEvent;
 -import java.awt.event.MouseEvent;
 -import java.awt.event.MouseListener;
 -import java.awt.event.MouseMotionListener;
 -import java.io.PrintStream;
 -import java.util.List;
 -import java.util.Vector;
 -
 -public class AppletPDBCanvas extends Panel
 -        implements MouseListener, MouseMotionListener, StructureListener
++public class AppletPDBCanvas
+ {
+ 
 -  MCMatrix idmat = new MCMatrix(3, 3);
 -
 -  MCMatrix objmat = new MCMatrix(3, 3);
 -
 -  boolean redrawneeded = true;
 -
 -  int omx = 0;
 -
 -  int mx = 0;
 -
 -  int omy = 0;
 -
 -  int my = 0;
 -
 -  public StructureFile pdb;
 -
 -  PDBEntry pdbentry;
 -
 -  int bsize;
 -
 -  Image img;
 -
 -  Graphics ig;
 -
 -  Dimension prefsize;
 -
 -  float[] centre = new float[3];
 -
 -  float[] width = new float[3];
 -
 -  float maxwidth;
 -
 -  float scale;
 -
 -  String inStr;
 -
 -  String inType;
 -
 -  boolean bysequence = true;
 -
 -  boolean depthcue = true;
 -
 -  boolean wire = false;
 -
 -  boolean bymolecule = false;
 -
 -  boolean zbuffer = true;
 -
 -  boolean dragging;
 -
 -  int xstart;
 -
 -  int xend;
 -
 -  int ystart;
 -
 -  int yend;
 -
 -  int xmid;
 -
 -  int ymid;
 -
 -  Font font = new Font("Helvetica", Font.PLAIN, 10);
 -
 -  public SequenceI[] sequence;
 -
 -  final StringBuffer mappingDetails = new StringBuffer();
 -
 -  String appletToolTip = null;
 -
 -  int toolx, tooly;
 -
 -  PDBChain mainchain;
 -
 -  Vector<String> highlightRes;
 -
 -  boolean pdbAction = false;
 -
 -  Bond highlightBond1, highlightBond2;
 -
 -  boolean errorLoading = false;
 -
 -  boolean seqColoursReady = false;
 -
 -  FeatureRenderer fr;
 -
 -  AlignmentPanel ap;
 -
 -  StructureSelectionManager ssm;
 -
 -  public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
 -          String[] chains, AlignmentPanel ap, DataSourceType protocol)
 -
 -  {
 -    this.ap = ap;
 -    this.pdbentry = pdbentry;
 -    this.sequence = seq;
 -
 -    ssm = StructureSelectionManager
 -            .getStructureSelectionManager(ap.av.applet);
 -
 -    try
 -    {
 -      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
 -
 -      if (protocol == DataSourceType.PASTE)
 -      {
 -        pdbentry.setFile("INLINE" + pdb.getId());
 -      }
 -
 -    } catch (Exception ex)
 -    {
 -      ex.printStackTrace();
 -      return;
 -    }
 -
 -    pdbentry.setId(pdb.getId());
 -
 -    ssm.addStructureViewerListener(this);
 -
 -    colourBySequence();
 -
 -    float max = -10;
 -    int maxchain = -1;
 -    int pdbstart = 0;
 -    int pdbend = 0;
 -    int seqstart = 0;
 -    int seqend = 0;
 -
 -    // JUST DEAL WITH ONE SEQUENCE FOR NOW
 -    SequenceI sequence = seq[0];
 -
 -    for (int i = 0; i < pdb.getChains().size(); i++)
 -    {
 -
 -      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
 -              + pdb.getChains().elementAt(i).sequence
 -                      .getSequenceAsString());
 -      mappingDetails.append("\nNo of residues = "
 -              + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 -
 -      // Now lets compare the sequences to get
 -      // the start and end points.
 -      // Align the sequence to the pdb
 -      // TODO: DNa/Pep switch
 -      AlignSeq as = new AlignSeq(sequence,
 -              pdb.getChains().elementAt(i).sequence,
 -              pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA
 -                      : AlignSeq.PEP);
 -      as.calcScoreMatrix();
 -      as.traceAlignment();
 -      PrintStream ps = new PrintStream(System.out)
 -      {
 -        @Override
 -        public void print(String x)
 -        {
 -          mappingDetails.append(x);
 -        }
 -
 -        @Override
 -        public void println()
 -        {
 -          mappingDetails.append("\n");
 -        }
 -      };
 -
 -      as.printAlignment(ps);
 -
 -      if (as.maxscore > max)
 -      {
 -        max = as.maxscore;
 -        maxchain = i;
 -
 -        pdbstart = as.seq2start;
 -        pdbend = as.seq2end;
 -        seqstart = as.seq1start + sequence.getStart() - 1;
 -        seqend = as.seq1end + sequence.getEnd() - 1;
 -      }
 -
 -      mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
 -      mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
 -    }
 -
 -    mainchain = pdb.getChains().elementAt(maxchain);
 -
 -    mainchain.pdbstart = pdbstart;
 -    mainchain.pdbend = pdbend;
 -    mainchain.seqstart = seqstart;
 -    mainchain.seqend = seqend;
 -    mainchain.isVisible = true;
 -    // mainchain.makeExactMapping(maxAlignseq, sequence);
 -    // mainchain.transferRESNUMFeatures(sequence, null);
 -    this.pdb = pdb;
 -    this.prefsize = new Dimension(getSize().width, getSize().height);
 -
 -    // Initialize the matrices to identity
 -    for (int i = 0; i < 3; i++)
 -    {
 -      for (int j = 0; j < 3; j++)
 -      {
 -        if (i != j)
 -        {
 -          idmat.addElement(i, j, 0);
 -          objmat.addElement(i, j, 0);
 -        }
 -        else
 -        {
 -          idmat.addElement(i, j, 1);
 -          objmat.addElement(i, j, 1);
 -        }
 -      }
 -    }
 -
 -    addMouseMotionListener(this);
 -    addMouseListener(this);
 -
 -    addKeyListener(new KeyAdapter()
 -    {
 -      @Override
 -      public void keyPressed(KeyEvent evt)
 -      {
 -        doKeyPressed(evt);
 -      }
 -    });
 -
 -    findCentre();
 -    findWidth();
 -
 -    setupBonds();
 -
 -    scale = findScale();
 -  }
 -
 -  Vector<Bond> visiblebonds;
 -
 -  void setupBonds()
 -  {
 -    seqColoursReady = false;
 -    // Sort the bonds by z coord
 -    visiblebonds = new Vector<Bond>();
 -
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      if (pdb.getChains().elementAt(ii).isVisible)
 -      {
 -        Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
 -
 -        for (int i = 0; i < tmp.size(); i++)
 -        {
 -          visiblebonds.addElement(tmp.elementAt(i));
 -        }
 -      }
 -    }
 -    seqColoursReady = true;
 -    colourBySequence();
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  public void findWidth()
 -  {
 -    float[] max = new float[3];
 -    float[] min = new float[3];
 -
 -    max[0] = (float) -1e30;
 -    max[1] = (float) -1e30;
 -    max[2] = (float) -1e30;
 -
 -    min[0] = (float) 1e30;
 -    min[1] = (float) 1e30;
 -    min[2] = (float) 1e30;
 -
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      if (pdb.getChains().elementAt(ii).isVisible)
 -      {
 -        Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
 -
 -        for (Bond tmp : bonds)
 -        {
 -          if (tmp.start[0] >= max[0])
 -          {
 -            max[0] = tmp.start[0];
 -          }
 -
 -          if (tmp.start[1] >= max[1])
 -          {
 -            max[1] = tmp.start[1];
 -          }
 -
 -          if (tmp.start[2] >= max[2])
 -          {
 -            max[2] = tmp.start[2];
 -          }
 -
 -          if (tmp.start[0] <= min[0])
 -          {
 -            min[0] = tmp.start[0];
 -          }
 -
 -          if (tmp.start[1] <= min[1])
 -          {
 -            min[1] = tmp.start[1];
 -          }
 -
 -          if (tmp.start[2] <= min[2])
 -          {
 -            min[2] = tmp.start[2];
 -          }
 -
 -          if (tmp.end[0] >= max[0])
 -          {
 -            max[0] = tmp.end[0];
 -          }
 -
 -          if (tmp.end[1] >= max[1])
 -          {
 -            max[1] = tmp.end[1];
 -          }
 -
 -          if (tmp.end[2] >= max[2])
 -          {
 -            max[2] = tmp.end[2];
 -          }
 -
 -          if (tmp.end[0] <= min[0])
 -          {
 -            min[0] = tmp.end[0];
 -          }
 -
 -          if (tmp.end[1] <= min[1])
 -          {
 -            min[1] = tmp.end[1];
 -          }
 -
 -          if (tmp.end[2] <= min[2])
 -          {
 -            min[2] = tmp.end[2];
 -          }
 -        }
 -      }
 -    }
 -
 -    width[0] = Math.abs(max[0] - min[0]);
 -    width[1] = Math.abs(max[1] - min[1]);
 -    width[2] = Math.abs(max[2] - min[2]);
 -
 -    maxwidth = width[0];
 -
 -    if (width[1] > width[0])
 -    {
 -      maxwidth = width[1];
 -    }
 -
 -    if (width[2] > width[1])
 -    {
 -      maxwidth = width[2];
 -    }
 -
 -    // System.out.println("Maxwidth = " + maxwidth);
 -  }
 -
 -  public float findScale()
 -  {
 -    int dim;
 -    int width;
 -    int height;
 -
 -    if (getSize().width != 0)
 -    {
 -      width = getSize().width;
 -      height = getSize().height;
 -    }
 -    else
 -    {
 -      width = prefsize.width;
 -      height = prefsize.height;
 -    }
 -
 -    if (width < height)
 -    {
 -      dim = width;
 -    }
 -    else
 -    {
 -      dim = height;
 -    }
 -
 -    return (float) (dim / (1.5d * maxwidth));
 -  }
 -
 -  public void findCentre()
 -  {
 -    float xtot = 0;
 -    float ytot = 0;
 -    float ztot = 0;
 -
 -    int bsize = 0;
 -
 -    // Find centre coordinate
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      if (pdb.getChains().elementAt(ii).isVisible)
 -      {
 -        Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
 -
 -        bsize += bonds.size();
 -
 -        for (Bond b : bonds)
 -        {
 -          xtot = xtot + b.start[0] + b.end[0];
 -          ytot = ytot + b.start[1] + b.end[1];
 -          ztot = ztot + b.start[2] + b.end[2];
 -        }
 -      }
 -    }
 -
 -    centre[0] = xtot / (2 * (float) bsize);
 -    centre[1] = ytot / (2 * (float) bsize);
 -    centre[2] = ztot / (2 * (float) bsize);
 -  }
 -
 -  @Override
 -  public void paint(Graphics g)
 -  {
 -
 -    if (errorLoading)
 -    {
 -      g.setColor(Color.white);
 -      g.fillRect(0, 0, getSize().width, getSize().height);
 -      g.setColor(Color.black);
 -      g.setFont(new Font("Verdana", Font.BOLD, 14));
 -      g.drawString(MessageManager.getString("label.error_loading_pdb_data"),
 -              50, getSize().height / 2);
 -      return;
 -    }
 -
 -    if (!seqColoursReady)
 -    {
 -      g.setColor(Color.black);
 -      g.setFont(new Font("Verdana", Font.BOLD, 14));
 -      g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
 -              getSize().height / 2);
 -      return;
 -    }
 -
 -    // Only create the image at the beginning -
 -    // this saves much memory usage
 -    if ((img == null) || (prefsize.width != getSize().width)
 -            || (prefsize.height != getSize().height))
 -    {
 -
 -      try
 -      {
 -        prefsize.width = getSize().width;
 -        prefsize.height = getSize().height;
 -
 -        scale = findScale();
 -        img = createImage(prefsize.width, prefsize.height);
 -        ig = img.getGraphics();
 -
 -        redrawneeded = true;
 -      } catch (Exception ex)
 -      {
 -        ex.printStackTrace();
 -      }
 -    }
 -
 -    if (redrawneeded)
 -    {
 -      drawAll(ig, prefsize.width, prefsize.height);
 -      redrawneeded = false;
 -    }
 -    if (appletToolTip != null)
 -    {
 -      ig.setColor(Color.red);
 -      ig.drawString(appletToolTip, toolx, tooly);
 -    }
 -
 -    g.drawImage(img, 0, 0, this);
 -
 -    pdbAction = false;
 -  }
 -
 -  public void drawAll(Graphics g, int width, int height)
 -  {
 -    ig.setColor(Color.black);
 -    ig.fillRect(0, 0, width, height);
 -    drawScene(ig);
 -    drawLabels(ig);
 -  }
 -
 -  public void setColours(jalview.schemes.ColourSchemeI cs)
 -  {
 -    bysequence = false;
 -    pdb.setColours(cs);
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  // This method has been taken out of PDBChain to allow
 -  // Applet and Application specific sequence renderers to be used
 -  void colourBySequence()
 -  {
 -    SequenceRenderer sr = new SequenceRenderer(ap.av);
 -
 -    StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 -
 -    boolean showFeatures = false;
 -    if (ap.av.isShowSequenceFeatures())
 -    {
 -      if (fr == null)
 -      {
 -        fr = new jalview.appletgui.FeatureRenderer(ap.av);
 -      }
 -
 -      fr.transferSettings(ap.getFeatureRenderer());
 -
 -      showFeatures = true;
 -    }
 -
 -    FeatureColourFinder finder = new FeatureColourFinder(fr);
 -
 -    PDBChain chain;
 -    if (bysequence && pdb != null)
 -    {
 -      for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -      {
 -        chain = pdb.getChains().elementAt(ii);
 -
 -        for (int i = 0; i < chain.bonds.size(); i++)
 -        {
 -          Bond tmp = chain.bonds.elementAt(i);
 -          tmp.startCol = Color.lightGray;
 -          tmp.endCol = Color.lightGray;
 -          if (chain != mainchain)
 -          {
 -            continue;
 -          }
 -
 -          for (int s = 0; s < sequence.length; s++)
 -          {
 -            for (int m = 0; m < mapping.length; m++)
 -            {
 -              if (mapping[m].getSequence() == sequence[s])
 -              {
 -                int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
 -                if (pos > 0)
 -                {
 -                  pos = sequence[s].findIndex(pos);
 -                  tmp.startCol = sr.getResidueColour(sequence[s], pos,
 -                          finder);
 -                }
 -                pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
 -                if (pos > 0)
 -                {
 -                  pos = sequence[s].findIndex(pos);
 -                  tmp.endCol = sr.getResidueColour(sequence[s], pos,
 -                          finder);
 -                }
 -              }
 -            }
 -          }
 -        }
 -      }
 -    }
 -  }
 -
 -  Zsort zsort;
 -
 -  public void drawScene(Graphics g)
 -  {
 -    if (zbuffer)
 -    {
 -      if (zsort == null)
 -      {
 -        zsort = new Zsort();
 -      }
 -
 -      zsort.sort(visiblebonds);
 -    }
 -
 -    Bond tmpBond = null;
 -    for (int i = 0; i < visiblebonds.size(); i++)
 -    {
 -      tmpBond = visiblebonds.elementAt(i);
 -
 -      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
 -              + (getSize().width / 2));
 -      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
 -              + (getSize().height / 2));
 -
 -      xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
 -              + (getSize().width / 2));
 -      yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
 -              + (getSize().height / 2));
 -
 -      xmid = (xend + xstart) / 2;
 -      ymid = (yend + ystart) / 2;
 -
 -      if (depthcue && !bymolecule)
 -      {
 -        if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
 -        {
 -          g.setColor(tmpBond.startCol.darker().darker());
 -          drawLine(g, xstart, ystart, xmid, ymid);
 -
 -          g.setColor(tmpBond.endCol.darker().darker());
 -          drawLine(g, xmid, ymid, xend, yend);
 -        }
 -        else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
 -        {
 -          g.setColor(tmpBond.startCol.darker());
 -          drawLine(g, xstart, ystart, xmid, ymid);
 -
 -          g.setColor(tmpBond.endCol.darker());
 -          drawLine(g, xmid, ymid, xend, yend);
 -        }
 -        else
 -        {
 -          g.setColor(tmpBond.startCol);
 -          drawLine(g, xstart, ystart, xmid, ymid);
 -
 -          g.setColor(tmpBond.endCol);
 -          drawLine(g, xmid, ymid, xend, yend);
 -        }
 -
 -      }
 -      else if (depthcue && bymolecule)
 -      {
 -        if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
 -        {
 -          g.setColor(Color.green.darker().darker());
 -          drawLine(g, xstart, ystart, xend, yend);
 -        }
 -        else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
 -        {
 -          g.setColor(Color.green.darker());
 -          drawLine(g, xstart, ystart, xend, yend);
 -        }
 -        else
 -        {
 -          g.setColor(Color.green);
 -          drawLine(g, xstart, ystart, xend, yend);
 -        }
 -      }
 -      else if (!depthcue && !bymolecule)
 -      {
 -        g.setColor(tmpBond.startCol);
 -        drawLine(g, xstart, ystart, xmid, ymid);
 -        g.setColor(tmpBond.endCol);
 -        drawLine(g, xmid, ymid, xend, yend);
 -      }
 -      else
 -      {
 -        drawLine(g, xstart, ystart, xend, yend);
 -      }
 -
 -      if (highlightBond1 != null && highlightBond1 == tmpBond)
 -      {
 -        g.setColor(Color.white);
 -        drawLine(g, xmid, ymid, xend, yend);
 -      }
 -
 -      if (highlightBond2 != null && highlightBond2 == tmpBond)
 -      {
 -        g.setColor(Color.white);
 -        drawLine(g, xstart, ystart, xmid, ymid);
 -      }
 -
 -    }
 -  }
 -
 -  public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
 -  {
 -    if (!wire)
 -    {
 -      if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
 -      {
 -        g.drawLine(x1, y1, x2, y2);
 -        g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
 -        g.drawLine(x1, y1 - 1, x2, y2 - 1);
 -      }
 -      else
 -      {
 -        g.setColor(g.getColor().brighter());
 -        g.drawLine(x1, y1, x2, y2);
 -        g.drawLine(x1 + 1, y1, x2 + 1, y2);
 -        g.drawLine(x1 - 1, y1, x2 - 1, y2);
 -      }
 -    }
 -    else
 -    {
 -      g.drawLine(x1, y1, x2, y2);
 -    }
 -  }
 -
 -  public Dimension minimumsize()
 -  {
 -    return prefsize;
 -  }
 -
 -  public Dimension preferredsize()
 -  {
 -    return prefsize;
 -  }
 -
 -  public void doKeyPressed(KeyEvent evt)
 -  {
 -    if (evt.getKeyCode() == KeyEvent.VK_UP)
 -    {
 -      scale = (float) (scale * 1.1);
 -      redrawneeded = true;
 -      repaint();
 -    }
 -    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
 -    {
 -      scale = (float) (scale * 0.9);
 -      redrawneeded = true;
 -      repaint();
 -    }
 -  }
 -
 -  @Override
 -  public void mousePressed(MouseEvent e)
 -  {
 -    pdbAction = true;
 -    Atom fatom = findAtom(e.getX(), e.getY());
 -    if (fatom != null)
 -    {
 -      fatom.isSelected = !fatom.isSelected;
 -
 -      redrawneeded = true;
 -      repaint();
 -      if (foundchain != -1)
 -      {
 -        PDBChain chain = pdb.getChains().elementAt(foundchain);
 -        if (chain == mainchain)
 -        {
 -          if (fatom.alignmentMapping != -1)
 -          {
 -            if (highlightRes == null)
 -            {
 -              highlightRes = new Vector<String>();
 -            }
 -
 -            final String atomString = Integer
 -                    .toString(fatom.alignmentMapping);
 -            if (highlightRes.contains(atomString))
 -            {
 -              highlightRes.removeElement(atomString);
 -            }
 -            else
 -            {
 -              highlightRes.addElement(atomString);
 -            }
 -          }
 -        }
 -      }
 -
 -    }
 -    mx = e.getX();
 -    my = e.getY();
 -    omx = mx;
 -    omy = my;
 -    dragging = false;
 -  }
 -
 -  @Override
 -  public void mouseMoved(MouseEvent e)
 -  {
 -    pdbAction = true;
 -    if (highlightBond1 != null)
 -    {
 -      highlightBond1.at2.isSelected = false;
 -      highlightBond2.at1.isSelected = false;
 -      highlightBond1 = null;
 -      highlightBond2 = null;
 -    }
 -
 -    Atom fatom = findAtom(e.getX(), e.getY());
 -
 -    PDBChain chain = null;
 -    if (foundchain != -1)
 -    {
 -      chain = pdb.getChains().elementAt(foundchain);
 -      if (chain == mainchain)
 -      {
 -        mouseOverStructure(fatom.resNumber, chain.id);
 -      }
 -    }
 -
 -    if (fatom != null)
 -    {
 -      toolx = e.getX();
 -      tooly = e.getY();
 -
 -      appletToolTip = chain.id + ":" + fatom.resNumber + " "
 -              + fatom.resName;
 -      redrawneeded = true;
 -      repaint();
 -    }
 -    else
 -    {
 -      mouseOverStructure(-1, chain != null ? chain.id : null);
 -      appletToolTip = null;
 -      redrawneeded = true;
 -      repaint();
 -    }
 -  }
 -
 -  @Override
 -  public void mouseClicked(MouseEvent e)
 -  {
 -  }
 -
 -  @Override
 -  public void mouseEntered(MouseEvent e)
 -  {
 -  }
 -
 -  @Override
 -  public void mouseExited(MouseEvent e)
 -  {
 -  }
 -
 -  @Override
 -  public void mouseDragged(MouseEvent evt)
 -  {
 -    int x = evt.getX();
 -    int y = evt.getY();
 -    mx = x;
 -    my = y;
 -
 -    MCMatrix objmat = new MCMatrix(3, 3);
 -    objmat.setIdentity();
 -
 -    if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
 -    {
 -      objmat.rotatez(((mx - omx)));
 -    }
 -    else
 -    {
 -      objmat.rotatex(((omy - my)));
 -      objmat.rotatey(((omx - mx)));
 -    }
 -
 -    // Alter the bonds
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      for (Bond tmpBond : chain.bonds)
 -      {
 -        // Translate the bond so the centre is 0,0,0
 -        tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 -
 -        // Now apply the rotation matrix
 -        tmpBond.start = objmat.vectorMultiply(tmpBond.start);
 -        tmpBond.end = objmat.vectorMultiply(tmpBond.end);
 -
 -        // Now translate back again
 -        tmpBond.translate(centre[0], centre[1], centre[2]);
 -      }
 -    }
 -
 -    objmat = null;
 -
 -    omx = mx;
 -    omy = my;
 -
 -    dragging = true;
 -
 -    redrawneeded = true;
 -
 -    repaint();
 -  }
 -
 -  @Override
 -  public void mouseReleased(MouseEvent evt)
 -  {
 -    dragging = false;
 -    return;
 -  }
 -
 -  void drawLabels(Graphics g)
 -  {
 -
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      if (chain.isVisible)
 -      {
 -        for (Bond tmpBond : chain.bonds)
 -        {
 -          if (tmpBond.at1.isSelected)
 -          {
 -            labelAtom(g, tmpBond, 1);
 -          }
 -
 -          if (tmpBond.at2.isSelected)
 -          {
 -            labelAtom(g, tmpBond, 2);
 -          }
 -        }
 -      }
 -    }
 -  }
 -
 -  public void labelAtom(Graphics g, Bond b, int n)
 -  {
 -    g.setFont(font);
 -
 -    if (n == 1)
 -    {
 -      int xstart = (int) (((b.start[0] - centre[0]) * scale)
 -              + (getSize().width / 2));
 -      int ystart = (int) (((centre[1] - b.start[1]) * scale)
 -              + (getSize().height / 2));
 -
 -      g.setColor(Color.red);
 -      g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
 -    }
 -
 -    if (n == 2)
 -    {
 -      int xstart = (int) (((b.end[0] - centre[0]) * scale)
 -              + (getSize().width / 2));
 -      int ystart = (int) (((centre[1] - b.end[1]) * scale)
 -              + (getSize().height / 2));
 -
 -      g.setColor(Color.red);
 -      g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
 -    }
 -  }
 -
 -  int foundchain = -1;
 -
 -  public Atom findAtom(int x, int y)
 -  {
 -    Atom fatom = null;
 -
 -    foundchain = -1;
 -
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      PDBChain chain = pdb.getChains().elementAt(ii);
 -      int truex;
 -      Bond tmpBond = null;
 -
 -      if (chain.isVisible)
 -      {
 -        Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
 -
 -        for (int i = 0; i < bonds.size(); i++)
 -        {
 -          tmpBond = bonds.elementAt(i);
 -
 -          truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
 -                  + (getSize().width / 2));
 -
 -          if (Math.abs(truex - x) <= 2)
 -          {
 -            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
 -                    + (getSize().height / 2));
 -
 -            if (Math.abs(truey - y) <= 2)
 -            {
 -              fatom = tmpBond.at1;
 -              foundchain = ii;
 -              break;
 -            }
 -          }
 -        }
 -
 -        // Still here? Maybe its the last bond
 -
 -        truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
 -                + (getSize().width / 2));
 -
 -        if (Math.abs(truex - x) <= 2)
 -        {
 -          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
 -                  + (getSize().height / 2));
 -
 -          if (Math.abs(truey - y) <= 2)
 -          {
 -            fatom = tmpBond.at2;
 -            foundchain = ii;
 -            break;
 -          }
 -        }
 -
 -      }
 -
 -      if (fatom != null) // )&& chain.ds != null)
 -      {
 -        chain = pdb.getChains().elementAt(foundchain);
 -      }
 -    }
 -
 -    return fatom;
 -  }
 -
 -  @Override
 -  public void update(Graphics g)
 -  {
 -    paint(g);
 -  }
 -
 -  public void highlightRes(int ii)
 -  {
 -    if (!seqColoursReady)
 -    {
 -      return;
 -    }
 -
 -    if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
 -    {
 -      return;
 -    }
 -
 -    int index = -1;
 -    Bond tmpBond;
 -    for (index = 0; index < mainchain.bonds.size(); index++)
 -    {
 -      tmpBond = mainchain.bonds.elementAt(index);
 -      if (tmpBond.at1.alignmentMapping == ii - 1)
 -      {
 -        if (highlightBond1 != null)
 -        {
 -          highlightBond1.at2.isSelected = false;
 -        }
 -
 -        if (highlightBond2 != null)
 -        {
 -          highlightBond2.at1.isSelected = false;
 -        }
 -
 -        highlightBond1 = null;
 -        highlightBond2 = null;
 -
 -        if (index > 0)
 -        {
 -          highlightBond1 = mainchain.bonds.elementAt(index - 1);
 -          highlightBond1.at2.isSelected = true;
 -        }
 -
 -        if (index != mainchain.bonds.size())
 -        {
 -          highlightBond2 = mainchain.bonds.elementAt(index);
 -          highlightBond2.at1.isSelected = true;
 -        }
 -
 -        break;
 -      }
 -    }
 -
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  public void setAllchainsVisible(boolean b)
 -  {
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      PDBChain chain = pdb.getChains().elementAt(ii);
 -      chain.isVisible = b;
 -    }
 -    mainchain.isVisible = true;
 -    findCentre();
 -    setupBonds();
 -  }
 -
 -  // ////////////////////////////////
 -  // /StructureListener
 -  @Override
 -  public String[] getStructureFiles()
 -  {
 -    return new String[] { pdbentry.getFile() };
 -  }
 -
 -  String lastMessage;
 -
 -  public void mouseOverStructure(int pdbResNum, String chain)
 -  {
 -    if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
 -    {
 -      ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
 -    }
 -
 -    lastMessage = pdbResNum + chain;
 -  }
 -
 -  StringBuffer resetLastRes = new StringBuffer();
 -
 -  StringBuffer eval = new StringBuffer();
 -
 -  /**
 -   * Highlight the specified atoms in the structure.
 -   * 
 -   * @param atoms
 -   */
 -  @Override
 -  public void highlightAtoms(List<AtomSpec> atoms)
 -  {
 -    if (!seqColoursReady)
 -    {
 -      return;
 -    }
 -    for (AtomSpec atom : atoms)
 -    {
 -      int atomIndex = atom.getAtomIndex();
 -
 -      if (highlightRes != null
 -              && highlightRes.contains((atomIndex - 1) + ""))
 -      {
 -        continue;
 -      }
 -
 -      highlightAtom(atomIndex);
 -    }
 -
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  /**
 -   * @param atomIndex
 -   */
 -  protected void highlightAtom(int atomIndex)
 -  {
 -    int index = -1;
 -    Bond tmpBond;
 -    for (index = 0; index < mainchain.bonds.size(); index++)
 -    {
 -      tmpBond = mainchain.bonds.elementAt(index);
 -      if (tmpBond.at1.atomIndex == atomIndex)
 -      {
 -        if (highlightBond1 != null)
 -        {
 -          highlightBond1.at2.isSelected = false;
 -        }
 -
 -        if (highlightBond2 != null)
 -        {
 -          highlightBond2.at1.isSelected = false;
 -        }
 -
 -        highlightBond1 = null;
 -        highlightBond2 = null;
 -
 -        if (index > 0)
 -        {
 -          highlightBond1 = mainchain.bonds.elementAt(index - 1);
 -          highlightBond1.at2.isSelected = true;
 -        }
 -
 -        if (index != mainchain.bonds.size())
 -        {
 -          highlightBond2 = mainchain.bonds.elementAt(index);
 -          highlightBond2.at1.isSelected = true;
 -        }
 -
 -        break;
 -      }
 -    }
 -  }
 -
 -  public Color getColour(int atomIndex, int pdbResNum, String chain,
 -          String pdbfile)
 -  {
 -    return Color.white;
 -    // if (!pdbfile.equals(pdbentry.getFile()))
 -    // return null;
 -
 -    // return new Color(viewer.getAtomArgb(atomIndex));
 -  }
 -
 -  @Override
 -  public void updateColours(Object source)
 -  {
 -    colourBySequence();
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  @Override
 -  public void releaseReferences(Object svl)
 -  {
 -    // TODO Auto-generated method stub
 -
 -  }
 -
 -  @Override
 -  public boolean isListeningFor(SequenceI seq)
 -  {
 -    if (sequence != null)
 -    {
 -      for (SequenceI s : sequence)
 -      {
 -        if (s == seq)
 -        {
 -          return true;
 -        }
 -      }
 -    }
 -    return false;
 -  }
+ }
diff --cc src/MCview/Atom.java
index 0000000,a2ce2ae..eb91e4e
mode 000000,100755..100644
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@@ -1,0 -1,136 +1,6 @@@
 -/*
 - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 - * Copyright (C) $$Year-Rel$$ The Jalview Authors
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3
 - * of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License
 - * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 - * The Jalview Authors are detailed in the 'AUTHORS' file.
 - */
+ package MCview;
+ 
 -import jalview.schemes.ResidueProperties;
 -
 -import java.awt.Color;
 -
+ public class Atom
+ {
 -  public float x;
 -
 -  public float y;
 -
 -  public float z;
 -
 -  public int number;
 -
 -  public String name;
 -
 -  public String resName;
 -
 -  public int resNumber;
 -
 -  public char insCode = ' ';
 -
 -  public String resNumIns = null;
 -
 -  public int type;
 -
 -  Color color = Color.lightGray;
 -
 -  public String chain;
 -
 -  /**
 -   * this is a temporary value - designed to store the position in sequence that
 -   * this atom corresponds to after aligning the chain to a SequenceI object. Do
 -   * not rely on its value being correct when visualizing sequence colourings on
 -   * the structure - use the StructureSelectionManager's mapping instead.
 -   */
 -  public int alignmentMapping = -1;
 -
 -  public int atomIndex;
 -
 -  public float occupancy = 0;
 -
 -  public float tfactor = 0;
 -
 -  // need these if we ever want to export Atom data
 -  // public boolean tfacset=true,occset=true;
 -  public boolean isSelected = false;
 -
 -  public Atom(String str)
 -  {
 -    atomIndex = Integer.parseInt(str.substring(6, 11).trim());
 -
 -    name = str.substring(12, 15).trim();
 -
 -    resName = str.substring(17, 20);
 -    // JAL-1828 treat MSE Selenomethionine as MET (etc)
 -    resName = ResidueProperties.getCanonicalAminoAcid(resName);
 -
 -    chain = str.substring(21, 22);
 -
 -    resNumber = Integer.parseInt(str.substring(22, 26).trim());
 -    resNumIns = str.substring(22, 27).trim();
 -    insCode = str.substring(26, 27).charAt(0);
 -    this.x = (Float.valueOf(str.substring(30, 38).trim()).floatValue());
 -    this.y = (Float.valueOf(str.substring(38, 46).trim()).floatValue());
 -    this.z = (Float.valueOf(str.substring(47, 55).trim()).floatValue());
 -    // optional entries - see JAL-730
 -    String tm = str.substring(54, 60).trim();
 -    if (tm.length() > 0)
 -    {
 -      occupancy = (Float.valueOf(tm)).floatValue();
 -    }
 -    else
 -    {
 -      occupancy = 1f; // default occupancy
 -      // see note above: occset=false;
 -    }
 -    tm = str.substring(60, 66).trim();
 -    if (tm.length() > 0)
 -    {
 -      tfactor = (Float.valueOf(tm).floatValue());
 -    }
 -    else
 -    {
 -      tfactor = 1f;
 -      // see note above: tfacset=false;
 -    }
 -  }
 -
 -  @Override
 -  public boolean equals(Object that)
 -  {
 -    if (this == that || that == null)
 -    {
 -      return true;
 -    }
 -    if (that instanceof Atom)
 -    {
 -      Atom other = (Atom) that;
 -      return other.resName.equals(this.resName)
 -              && other.resNumber == this.resNumber
 -              && other.resNumIns.equals(this.resNumIns)
 -              && other.chain.equals(this.chain);
 -    }
 -    return false;
 -  }
+ 
 -  public Atom(float x, float y, float z)
 -  {
 -    this.x = x;
 -    this.y = y;
 -    this.z = z;
 -  }
+ }
diff --cc src/MCview/PDBCanvas.java
index 0000000,a34e574..c49ab09
mode 000000,100644..100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@@ -1,0 -1,1223 +1,6 @@@
 -/*
 - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 - * Copyright (C) $$Year-Rel$$ The Jalview Authors
 - * 
 - * This file is part of Jalview.
 - * 
 - * Jalview is free software: you can redistribute it and/or
 - * modify it under the terms of the GNU General Public License 
 - * as published by the Free Software Foundation, either version 3
 - * of the License, or (at your option) any later version.
 - *  
 - * Jalview is distributed in the hope that it will be useful, but 
 - * WITHOUT ANY WARRANTY; without even the implied warranty 
 - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 - * PURPOSE.  See the GNU General Public License for more details.
 - * 
 - * You should have received a copy of the GNU General Public License
 - * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 - * The Jalview Authors are detailed in the 'AUTHORS' file.
 - */
+ package MCview;
+ 
 -import jalview.analysis.AlignSeq;
 -import jalview.datamodel.PDBEntry;
 -import jalview.datamodel.SequenceI;
 -import jalview.gui.AlignmentPanel;
 -import jalview.gui.FeatureRenderer;
 -import jalview.gui.SequenceRenderer;
 -import jalview.io.DataSourceType;
 -import jalview.io.StructureFile;
 -import jalview.renderer.seqfeatures.FeatureColourFinder;
 -import jalview.structure.AtomSpec;
 -import jalview.structure.StructureListener;
 -import jalview.structure.StructureMapping;
 -import jalview.structure.StructureSelectionManager;
 -
 -import java.awt.Color;
 -import java.awt.Dimension;
 -import java.awt.event.InputEvent;import java.awt.Font;
 -import java.awt.Graphics;
 -import java.awt.Graphics2D;
 -// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
 -import java.awt.Image;
 -import java.awt.RenderingHints;
 -import java.awt.event.KeyAdapter;
 -import java.awt.event.KeyEvent;
 -import java.awt.event.MouseEvent;
 -import java.awt.event.MouseListener;
 -import java.awt.event.MouseMotionListener;
 -import java.io.PrintStream;
 -import java.util.List;
 -import java.util.Vector;
 -
 -import javax.swing.JPanel;
 -import javax.swing.ToolTipManager;
 -
 -public class PDBCanvas extends JPanel
 -        implements MouseListener, MouseMotionListener, StructureListener
++public class PDBCanvas
+ {
 -  boolean redrawneeded = true;
 -
 -  int omx = 0;
 -
 -  int mx = 0;
 -
 -  int omy = 0;
 -
 -  int my = 0;
 -
 -  public StructureFile pdb;
 -
 -  PDBEntry pdbentry;
 -
 -  int bsize;
 -
 -  Image img;
 -
 -  Graphics ig;
 -
 -  Dimension prefsize;
 -
 -  float[] centre = new float[3];
 -
 -  float[] width = new float[3];
 -
 -  float maxwidth;
 -
 -  float scale;
 -
 -  String inStr;
 -
 -  String inType;
 -
 -  boolean bysequence = true;
 -
 -  boolean depthcue = true;
 -
 -  boolean wire = false;
 -
 -  boolean bymolecule = false;
 -
 -  boolean zbuffer = true;
 -
 -  boolean dragging;
 -
 -  int xstart;
 -
 -  int xend;
 -
 -  int ystart;
 -
 -  int yend;
 -
 -  int xmid;
 -
 -  int ymid;
 -
 -  Font font = new Font("Helvetica", Font.PLAIN, 10);
 -
 -  jalview.gui.SeqCanvas seqcanvas;
 -
 -  public SequenceI[] sequence;
 -
 -  final StringBuffer mappingDetails = new StringBuffer();
 -
 -  PDBChain mainchain;
 -
 -  Vector<String> highlightRes;
 -
 -  boolean pdbAction = false;
 -
 -  boolean seqColoursReady = false;
 -
 -  jalview.renderer.seqfeatures.FeatureRenderer fr;
 -
 -  Color backgroundColour = Color.black;
 -
 -  AlignmentPanel ap;
 -
 -  StructureSelectionManager ssm;
 -
 -  String errorMessage;
 -
 -  void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
 -          AlignmentPanel ap, DataSourceType protocol)
 -  {
 -    this.ap = ap;
 -    this.pdbentry = pdbentry;
 -    this.sequence = seq;
 -
 -    ssm = ap.av.getStructureSelectionManager();
 -
 -    try
 -    {
 -      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
 -              ap.alignFrame);
 -
 -      if (protocol.equals(jalview.io.DataSourceType.PASTE))
 -      {
 -        pdbentry.setFile("INLINE" + pdb.getId());
 -      }
 -
 -    } catch (Exception ex)
 -    {
 -      ex.printStackTrace();
 -      return;
 -    }
 -
 -    if (pdb == null)
 -    {
 -      errorMessage = "Error loading file: " + pdbentry.getId();
 -      return;
 -    }
 -    pdbentry.setId(pdb.getId());
 -
 -    ssm.addStructureViewerListener(this);
 -
 -    colourBySequence();
 -
 -    float max = -10;
 -    int maxchain = -1;
 -    int pdbstart = 0;
 -    int pdbend = 0;
 -    int seqstart = 0;
 -    int seqend = 0;
 -
 -    // JUST DEAL WITH ONE SEQUENCE FOR NOW
 -    SequenceI sequence = seq[0];
 -
 -    for (int i = 0; i < pdb.getChains().size(); i++)
 -    {
 -
 -      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
 -              + pdb.getChains().elementAt(i).sequence
 -                      .getSequenceAsString());
 -      mappingDetails.append("\nNo of residues = "
 -              + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 -
 -      // Now lets compare the sequences to get
 -      // the start and end points.
 -      // Align the sequence to the pdb
 -      AlignSeq as = new AlignSeq(sequence,
 -              pdb.getChains().elementAt(i).sequence, "pep");
 -      as.calcScoreMatrix();
 -      as.traceAlignment();
 -      PrintStream ps = new PrintStream(System.out)
 -      {
 -        @Override
 -        public void print(String x)
 -        {
 -          mappingDetails.append(x);
 -        }
 -
 -        @Override
 -        public void println()
 -        {
 -          mappingDetails.append("\n");
 -        }
 -      };
 -
 -      as.printAlignment(ps);
 -
 -      if (as.maxscore > max)
 -      {
 -        max = as.maxscore;
 -        maxchain = i;
 -
 -        pdbstart = as.seq2start;
 -        pdbend = as.seq2end;
 -        seqstart = as.seq1start + sequence.getStart() - 1;
 -        seqend = as.seq1end + sequence.getEnd() - 1;
 -      }
 -
 -      mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
 -      mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
 -    }
 -
 -    mainchain = pdb.getChains().elementAt(maxchain);
 -
 -    mainchain.pdbstart = pdbstart;
 -    mainchain.pdbend = pdbend;
 -    mainchain.seqstart = seqstart;
 -    mainchain.seqend = seqend;
 -    mainchain.isVisible = true;
 -
 -    this.pdb = pdb;
 -    this.prefsize = new Dimension(getSize().width, getSize().height);
 -
 -    addMouseMotionListener(this);
 -    addMouseListener(this);
 -
 -    addKeyListener(new KeyAdapter()
 -    {
 -      @Override
 -      public void keyPressed(KeyEvent evt)
 -      {
 -        keyPressed(evt);
 -      }
 -    });
 -
 -    findCentre();
 -    findWidth();
 -
 -    setupBonds();
 -
 -    scale = findScale();
 -
 -    ToolTipManager.sharedInstance().registerComponent(this);
 -    ToolTipManager.sharedInstance().setInitialDelay(0);
 -    ToolTipManager.sharedInstance().setDismissDelay(10000);
 -  }
 -
 -  Vector<Bond> visiblebonds;
 -
 -  void setupBonds()
 -  {
 -    seqColoursReady = false;
 -    // Sort the bonds by z coord
 -    visiblebonds = new Vector<Bond>();
 -
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      if (chain.isVisible)
 -      {
 -        for (Bond bond : chain.bonds)
 -        {
 -          visiblebonds.addElement(bond);
 -        }
 -      }
 -    }
 -
 -    updateSeqColours();
 -    seqColoursReady = true;
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  public void findWidth()
 -  {
 -    float[] max = new float[3];
 -    float[] min = new float[3];
 -
 -    max[0] = (float) -1e30;
 -    max[1] = (float) -1e30;
 -    max[2] = (float) -1e30;
 -
 -    min[0] = (float) 1e30;
 -    min[1] = (float) 1e30;
 -    min[2] = (float) 1e30;
 -
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      if (chain.isVisible)
 -      {
 -        for (Bond tmp : chain.bonds)
 -        {
 -          if (tmp.start[0] >= max[0])
 -          {
 -            max[0] = tmp.start[0];
 -          }
 -
 -          if (tmp.start[1] >= max[1])
 -          {
 -            max[1] = tmp.start[1];
 -          }
 -
 -          if (tmp.start[2] >= max[2])
 -          {
 -            max[2] = tmp.start[2];
 -          }
 -
 -          if (tmp.start[0] <= min[0])
 -          {
 -            min[0] = tmp.start[0];
 -          }
 -
 -          if (tmp.start[1] <= min[1])
 -          {
 -            min[1] = tmp.start[1];
 -          }
 -
 -          if (tmp.start[2] <= min[2])
 -          {
 -            min[2] = tmp.start[2];
 -          }
 -
 -          if (tmp.end[0] >= max[0])
 -          {
 -            max[0] = tmp.end[0];
 -          }
 -
 -          if (tmp.end[1] >= max[1])
 -          {
 -            max[1] = tmp.end[1];
 -          }
 -
 -          if (tmp.end[2] >= max[2])
 -          {
 -            max[2] = tmp.end[2];
 -          }
 -
 -          if (tmp.end[0] <= min[0])
 -          {
 -            min[0] = tmp.end[0];
 -          }
 -
 -          if (tmp.end[1] <= min[1])
 -          {
 -            min[1] = tmp.end[1];
 -          }
 -
 -          if (tmp.end[2] <= min[2])
 -          {
 -            min[2] = tmp.end[2];
 -          }
 -        }
 -      }
 -    }
 -    /*
 -     * System.out.println("xmax " + max[0] + " min " + min[0]);
 -     * System.out.println("ymax " + max[1] + " min " + min[1]);
 -     * System.out.println("zmax " + max[2] + " min " + min[2]);
 -     */
 -
 -    width[0] = Math.abs(max[0] - min[0]);
 -    width[1] = Math.abs(max[1] - min[1]);
 -    width[2] = Math.abs(max[2] - min[2]);
 -
 -    maxwidth = width[0];
 -
 -    if (width[1] > width[0])
 -    {
 -      maxwidth = width[1];
 -    }
 -
 -    if (width[2] > width[1])
 -    {
 -      maxwidth = width[2];
 -    }
 -
 -    // System.out.println("Maxwidth = " + maxwidth);
 -  }
 -
 -  public float findScale()
 -  {
 -    int dim;
 -    int width;
 -    int height;
 -
 -    if (getWidth() != 0)
 -    {
 -      width = getWidth();
 -      height = getHeight();
 -    }
 -    else
 -    {
 -      width = prefsize.width;
 -      height = prefsize.height;
 -    }
 -
 -    if (width < height)
 -    {
 -      dim = width;
 -    }
 -    else
 -    {
 -      dim = height;
 -    }
 -
 -    return (float) (dim / (1.5d * maxwidth));
 -  }
 -
 -  public void findCentre()
 -  {
 -    float xtot = 0;
 -    float ytot = 0;
 -    float ztot = 0;
 -
 -    int bsize = 0;
 -
 -    // Find centre coordinate
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      if (chain.isVisible)
 -      {
 -        bsize += chain.bonds.size();
 -
 -        for (Bond bond : chain.bonds)
 -        {
 -          xtot = xtot + bond.start[0] + bond.end[0];
 -          ytot = ytot + bond.start[1] + bond.end[1];
 -          ztot = ztot + bond.start[2] + bond.end[2];
 -        }
 -      }
 -    }
 -
 -    centre[0] = xtot / (2 * (float) bsize);
 -    centre[1] = ytot / (2 * (float) bsize);
 -    centre[2] = ztot / (2 * (float) bsize);
 -  }
 -
 -  @Override
 -  public void paintComponent(Graphics g)
 -  {
 -    super.paintComponent(g);
 -
 -    if (!seqColoursReady || errorMessage != null)
 -    {
 -      g.setColor(Color.black);
 -      g.setFont(new Font("Verdana", Font.BOLD, 14));
 -      g.drawString(errorMessage == null ? "Retrieving PDB data...."
 -              : errorMessage, 20, getHeight() / 2);
 -      return;
 -    }
 -
 -    // Only create the image at the beginning -
 -    // this saves much memory usage
 -    if ((img == null) || (prefsize.width != getWidth())
 -            || (prefsize.height != getHeight()))
 -
 -    {
 -      prefsize.width = getWidth();
 -      prefsize.height = getHeight();
 -
 -      scale = findScale();
 -      img = createImage(prefsize.width, prefsize.height);
 -      ig = img.getGraphics();
 -      Graphics2D ig2 = (Graphics2D) ig;
 -
 -      ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
 -              RenderingHints.VALUE_ANTIALIAS_ON);
 -
 -      redrawneeded = true;
 -    }
 -
 -    if (redrawneeded)
 -    {
 -      drawAll(ig, prefsize.width, prefsize.height);
 -      redrawneeded = false;
 -    }
 -
 -    g.drawImage(img, 0, 0, this);
 -
 -    pdbAction = false;
 -  }
 -
 -  public void drawAll(Graphics g, int width, int height)
 -  {
 -    g.setColor(backgroundColour);
 -    g.fillRect(0, 0, width, height);
 -    drawScene(g);
 -    drawLabels(g);
 -  }
 -
 -  public void updateSeqColours()
 -  {
 -    if (pdbAction)
 -    {
 -      return;
 -    }
 -
 -    colourBySequence();
 -
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  // This method has been taken out of PDBChain to allow
 -  // Applet and Application specific sequence renderers to be used
 -  void colourBySequence()
 -  {
 -    SequenceRenderer sr = new SequenceRenderer(ap.av);
 -
 -    StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 -
 -    boolean showFeatures = false;
 -    if (ap.av.isShowSequenceFeatures())
 -    {
 -      if (fr == null)
 -      {
 -        fr = new FeatureRenderer(ap);
 -      }
 -
 -      fr.transferSettings(ap.alignFrame.getFeatureRenderer());
 -
 -      showFeatures = true;
 -    }
 -
 -    FeatureColourFinder finder = new FeatureColourFinder(fr);
 -    PDBChain chain;
 -    if (bysequence && pdb != null)
 -    {
 -      for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -      {
 -        chain = pdb.getChains().elementAt(ii);
 -
 -        for (int i = 0; i < chain.bonds.size(); i++)
 -        {
 -          Bond tmp = chain.bonds.elementAt(i);
 -          tmp.startCol = Color.lightGray;
 -          tmp.endCol = Color.lightGray;
 -          if (chain != mainchain)
 -          {
 -            continue;
 -          }
 -
 -          for (int s = 0; s < sequence.length; s++)
 -          {
 -            for (int m = 0; m < mapping.length; m++)
 -            {
 -              if (mapping[m].getSequence() == sequence[s])
 -              {
 -                int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
 -                if (pos > 0)
 -                {
 -                  pos = sequence[s].findIndex(pos);
 -                  tmp.startCol = sr.getResidueColour(sequence[s], pos,
 -                          finder);
 -                }
 -                pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
 -                if (pos > 0)
 -                {
 -                  pos = sequence[s].findIndex(pos);
 -                  tmp.endCol = sr.getResidueColour(sequence[s], pos,
 -                          finder);
 -                }
 -
 -              }
 -            }
 -          }
 -        }
 -      }
 -    }
 -  }
 -
 -  Zsort zsort;
 -
 -  public void drawScene(Graphics g)
 -  {
 -    if (zbuffer)
 -    {
 -      if (zsort == null)
 -      {
 -        zsort = new Zsort();
 -      }
 -
 -      zsort.sort(visiblebonds);
 -    }
 -
 -    Bond tmpBond = null;
 -    for (int i = 0; i < visiblebonds.size(); i++)
 -    {
 -      tmpBond = visiblebonds.elementAt(i);
 -
 -      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
 -              + (getWidth() / 2));
 -      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
 -              + (getHeight() / 2));
 -
 -      xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
 -              + (getWidth() / 2));
 -      yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
 -              + (getHeight() / 2));
 -
 -      xmid = (xend + xstart) / 2;
 -      ymid = (yend + ystart) / 2;
 -      if (depthcue && !bymolecule)
 -      {
 -        if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
 -        {
 -
 -          g.setColor(tmpBond.startCol.darker().darker());
 -          drawLine(g, xstart, ystart, xmid, ymid);
 -          g.setColor(tmpBond.endCol.darker().darker());
 -          drawLine(g, xmid, ymid, xend, yend);
 -
 -        }
 -        else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
 -        {
 -          g.setColor(tmpBond.startCol.darker());
 -          drawLine(g, xstart, ystart, xmid, ymid);
 -
 -          g.setColor(tmpBond.endCol.darker());
 -          drawLine(g, xmid, ymid, xend, yend);
 -        }
 -        else
 -        {
 -          g.setColor(tmpBond.startCol);
 -          drawLine(g, xstart, ystart, xmid, ymid);
 -
 -          g.setColor(tmpBond.endCol);
 -          drawLine(g, xmid, ymid, xend, yend);
 -        }
 -      }
 -      else if (depthcue && bymolecule)
 -      {
 -        if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
 -        {
 -          g.setColor(Color.green.darker().darker());
 -          drawLine(g, xstart, ystart, xend, yend);
 -        }
 -        else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
 -        {
 -          g.setColor(Color.green.darker());
 -          drawLine(g, xstart, ystart, xend, yend);
 -        }
 -        else
 -        {
 -          g.setColor(Color.green);
 -          drawLine(g, xstart, ystart, xend, yend);
 -        }
 -      }
 -      else if (!depthcue && !bymolecule)
 -      {
 -        g.setColor(tmpBond.startCol);
 -        drawLine(g, xstart, ystart, xmid, ymid);
 -        g.setColor(tmpBond.endCol);
 -        drawLine(g, xmid, ymid, xend, yend);
 -      }
 -      else
 -      {
 -        drawLine(g, xstart, ystart, xend, yend);
 -      }
 -
 -      if (highlightBond1 != null && highlightBond1 == tmpBond)
 -      {
 -        g.setColor(
 -                tmpBond.endCol.brighter().brighter().brighter().brighter());
 -        drawLine(g, xmid, ymid, xend, yend);
 -      }
 -
 -      if (highlightBond2 != null && highlightBond2 == tmpBond)
 -      {
 -        g.setColor(tmpBond.startCol.brighter().brighter().brighter()
 -                .brighter());
 -        drawLine(g, xstart, ystart, xmid, ymid);
 -      }
 -
 -    }
 -
 -  }
 -
 -  public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
 -  {
 -    if (!wire)
 -    {
 -      if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
 -      {
 -        g.drawLine(x1, y1, x2, y2);
 -        g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
 -        g.drawLine(x1, y1 - 1, x2, y2 - 1);
 -      }
 -      else
 -      {
 -        g.setColor(g.getColor().brighter());
 -        g.drawLine(x1, y1, x2, y2);
 -        g.drawLine(x1 + 1, y1, x2 + 1, y2);
 -        g.drawLine(x1 - 1, y1, x2 - 1, y2);
 -      }
 -    }
 -    else
 -    {
 -      g.drawLine(x1, y1, x2, y2);
 -    }
 -  }
 -
 -  public Dimension minimumsize()
 -  {
 -    return prefsize;
 -  }
 -
 -  public Dimension preferredsize()
 -  {
 -    return prefsize;
 -  }
 -
 -  public void keyPressed(KeyEvent evt)
 -  {
 -    if (evt.getKeyCode() == KeyEvent.VK_UP)
 -    {
 -      scale = (float) (scale * 1.1);
 -      redrawneeded = true;
 -      repaint();
 -    }
 -    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
 -    {
 -      scale = (float) (scale * 0.9);
 -      redrawneeded = true;
 -      repaint();
 -    }
 -  }
 -
 -  @Override
 -  public void mousePressed(MouseEvent e)
 -  {
 -    pdbAction = true;
 -    Atom fatom = findAtom(e.getX(), e.getY());
 -    if (fatom != null)
 -    {
 -      fatom.isSelected = !fatom.isSelected;
 -
 -      redrawneeded = true;
 -      repaint();
 -      if (foundchain != -1)
 -      {
 -        PDBChain chain = pdb.getChains().elementAt(foundchain);
 -        if (chain == mainchain)
 -        {
 -          if (fatom.alignmentMapping != -1)
 -          {
 -            if (highlightRes == null)
 -            {
 -              highlightRes = new Vector<String>();
 -            }
 -
 -            final String atomString = Integer
 -                    .toString(fatom.alignmentMapping);
 -            if (highlightRes.contains(atomString))
 -            {
 -              highlightRes.remove(atomString);
 -            }
 -            else
 -            {
 -              highlightRes.add(atomString);
 -            }
 -          }
 -        }
 -      }
 -
 -    }
 -    mx = e.getX();
 -    my = e.getY();
 -    omx = mx;
 -    omy = my;
 -    dragging = false;
 -  }
 -
 -  @Override
 -  public void mouseMoved(MouseEvent e)
 -  {
 -    pdbAction = true;
 -    if (highlightBond1 != null)
 -    {
 -      highlightBond1.at2.isSelected = false;
 -      highlightBond2.at1.isSelected = false;
 -      highlightBond1 = null;
 -      highlightBond2 = null;
 -    }
 -
 -    Atom fatom = findAtom(e.getX(), e.getY());
 -
 -    PDBChain chain = null;
 -    if (foundchain != -1)
 -    {
 -      chain = pdb.getChains().elementAt(foundchain);
 -      if (chain == mainchain)
 -      {
 -        mouseOverStructure(fatom.resNumber, chain.id);
 -      }
 -    }
 -
 -    if (fatom != null)
 -    {
 -      this.setToolTipText(
 -              chain.id + ":" + fatom.resNumber + " " + fatom.resName);
 -    }
 -    else
 -    {
 -      mouseOverStructure(-1, chain != null ? chain.id : null);
 -      this.setToolTipText(null);
 -    }
 -  }
 -
 -  @Override
 -  public void mouseClicked(MouseEvent e)
 -  {
 -  }
 -
 -  @Override
 -  public void mouseEntered(MouseEvent e)
 -  {
 -  }
 -
 -  @Override
 -  public void mouseExited(MouseEvent e)
 -  {
 -  }
 -
 -  @Override
 -  public void mouseDragged(MouseEvent evt)
 -  {
 -    int x = evt.getX();
 -    int y = evt.getY();
 -    mx = x;
 -    my = y;
 -
 -    MCMatrix objmat = new MCMatrix(3, 3);
 -    objmat.setIdentity();
 -
 -    if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
 -    {
 -      objmat.rotatez(((mx - omx)));
 -    }
 -    else
 -    {
 -      objmat.rotatex(((my - omy)));
 -      objmat.rotatey(((omx - mx)));
 -    }
 -
 -    // Alter the bonds
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      for (Bond tmpBond : chain.bonds)
 -      {
 -        // Translate the bond so the centre is 0,0,0
 -        tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 -
 -        // Now apply the rotation matrix
 -        tmpBond.start = objmat.vectorMultiply(tmpBond.start);
 -        tmpBond.end = objmat.vectorMultiply(tmpBond.end);
 -
 -        // Now translate back again
 -        tmpBond.translate(centre[0], centre[1], centre[2]);
 -      }
 -    }
 -
 -    objmat = null;
 -
 -    omx = mx;
 -    omy = my;
 -
 -    dragging = true;
 -
 -    redrawneeded = true;
 -
 -    repaint();
 -  }
 -
 -  @Override
 -  public void mouseReleased(MouseEvent evt)
 -  {
 -    dragging = false;
 -    return;
 -  }
 -
 -  void drawLabels(Graphics g)
 -  {
 -
 -    for (PDBChain chain : pdb.getChains())
 -    {
 -      if (chain.isVisible)
 -      {
 -        for (Bond tmpBond : chain.bonds)
 -        {
 -          if (tmpBond.at1.isSelected)
 -          {
 -            labelAtom(g, tmpBond, 1);
 -          }
 -
 -          if (tmpBond.at2.isSelected)
 -          {
 -            labelAtom(g, tmpBond, 2);
 -          }
 -        }
 -      }
 -    }
 -  }
 -
 -  public void labelAtom(Graphics g, Bond b, int n)
 -  {
 -    g.setFont(font);
 -    g.setColor(Color.red);
 -    if (n == 1)
 -    {
 -      int xstart = (int) (((b.start[0] - centre[0]) * scale)
 -              + (getWidth() / 2));
 -      int ystart = (int) (((centre[1] - b.start[1]) * scale)
 -              + (getHeight() / 2));
 -
 -      g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
 -    }
 -
 -    if (n == 2)
 -    {
 -      int xstart = (int) (((b.end[0] - centre[0]) * scale)
 -              + (getWidth() / 2));
 -      int ystart = (int) (((centre[1] - b.end[1]) * scale)
 -              + (getHeight() / 2));
 -
 -      g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
 -    }
 -  }
 -
 -  int foundchain = -1;
 -
 -  public Atom findAtom(int x, int y)
 -  {
 -    Atom fatom = null;
 -
 -    foundchain = -1;
 -
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      PDBChain chain = pdb.getChains().elementAt(ii);
 -      int truex;
 -      Bond tmpBond = null;
 -
 -      if (chain.isVisible)
 -      {
 -        for (Bond bond : chain.bonds)
 -        {
 -          tmpBond = bond;
 -
 -          truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
 -                  + (getWidth() / 2));
 -
 -          if (Math.abs(truex - x) <= 2)
 -          {
 -            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
 -                    + (getHeight() / 2));
 -
 -            if (Math.abs(truey - y) <= 2)
 -            {
 -              fatom = tmpBond.at1;
 -              foundchain = ii;
 -              break;
 -            }
 -          }
 -        }
 -
 -        // Still here? Maybe its the last bond
 -
 -        truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
 -                + (getWidth() / 2));
 -
 -        if (Math.abs(truex - x) <= 2)
 -        {
 -          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
 -                  + (getHeight() / 2));
 -
 -          if (Math.abs(truey - y) <= 2)
 -          {
 -            fatom = tmpBond.at2;
 -            foundchain = ii;
 -            break;
 -          }
 -        }
 -
 -      }
 -
 -      if (fatom != null) // )&& chain.ds != null)
 -      { // dead code? value of chain is either overwritten or discarded
 -        chain = pdb.getChains().elementAt(foundchain);
 -      }
 -    }
 -
 -    return fatom;
 -  }
 -
 -  Bond highlightBond1, highlightBond2;
 -
 -  public void highlightRes(int ii)
 -  {
 -    if (!seqColoursReady)
 -    {
 -      return;
 -    }
 -
 -    if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
 -    {
 -      return;
 -    }
 -
 -    int index = -1;
 -    Bond tmpBond;
 -    for (index = 0; index < mainchain.bonds.size(); index++)
 -    {
 -      tmpBond = mainchain.bonds.elementAt(index);
 -      if (tmpBond.at1.alignmentMapping == ii - 1)
 -      {
 -        if (highlightBond1 != null)
 -        {
 -          highlightBond1.at2.isSelected = false;
 -        }
 -
 -        if (highlightBond2 != null)
 -        {
 -          highlightBond2.at1.isSelected = false;
 -        }
 -
 -        highlightBond1 = null;
 -        highlightBond2 = null;
 -
 -        if (index > 0)
 -        {
 -          highlightBond1 = mainchain.bonds.elementAt(index - 1);
 -          highlightBond1.at2.isSelected = true;
 -        }
 -
 -        if (index != mainchain.bonds.size())
 -        {
 -          highlightBond2 = mainchain.bonds.elementAt(index);
 -          highlightBond2.at1.isSelected = true;
 -        }
 -
 -        break;
 -      }
 -    }
 -
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  public void setAllchainsVisible(boolean b)
 -  {
 -    for (int ii = 0; ii < pdb.getChains().size(); ii++)
 -    {
 -      PDBChain chain = pdb.getChains().elementAt(ii);
 -      chain.isVisible = b;
 -    }
 -    mainchain.isVisible = true;
 -    findCentre();
 -    setupBonds();
 -  }
 -
 -  // ////////////////////////////////
 -  // /StructureListener
 -  @Override
 -  public String[] getStructureFiles()
 -  {
 -    return new String[] { pdbentry.getFile() };
 -  }
 -
 -  String lastMessage;
 -
 -  public void mouseOverStructure(int pdbResNum, String chain)
 -  {
 -    if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
 -    {
 -      ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
 -    }
 -
 -    lastMessage = pdbResNum + chain;
 -  }
 -
 -  StringBuffer resetLastRes = new StringBuffer();
 -
 -  StringBuffer eval = new StringBuffer();
 -
 -  /**
 -   * Highlight the specified atoms in the structure.
 -   * 
 -   * @param atoms
 -   */
 -  @Override
 -  public void highlightAtoms(List<AtomSpec> atoms)
 -  {
 -    if (!seqColoursReady)
 -    {
 -      return;
 -    }
 -
 -    for (AtomSpec atom : atoms)
 -    {
 -      int atomIndex = atom.getAtomIndex();
 -      if (highlightRes != null
 -              && highlightRes.contains((atomIndex - 1) + ""))
 -      {
 -        continue;
 -      }
 -
 -      highlightAtom(atomIndex);
 -    }
 -
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  /**
 -   * Highlight the atom at the specified index.
 -   * 
 -   * @param atomIndex
 -   */
 -  protected void highlightAtom(int atomIndex)
 -  {
 -    int index = -1;
 -    Bond tmpBond;
 -    for (index = 0; index < mainchain.bonds.size(); index++)
 -    {
 -      tmpBond = mainchain.bonds.elementAt(index);
 -      if (tmpBond.at1.atomIndex == atomIndex)
 -      {
 -        if (highlightBond1 != null)
 -        {
 -          highlightBond1.at2.isSelected = false;
 -        }
 -
 -        if (highlightBond2 != null)
 -        {
 -          highlightBond2.at1.isSelected = false;
 -        }
 -
 -        highlightBond1 = null;
 -        highlightBond2 = null;
 -
 -        if (index > 0)
 -        {
 -          highlightBond1 = mainchain.bonds.elementAt(index - 1);
 -          highlightBond1.at2.isSelected = true;
 -        }
 -
 -        if (index != mainchain.bonds.size())
 -        {
 -          highlightBond2 = mainchain.bonds.elementAt(index);
 -          highlightBond2.at1.isSelected = true;
 -        }
 -
 -        break;
 -      }
 -    }
 -  }
 -
 -  public Color getColour(int atomIndex, int pdbResNum, String chain,
 -          String pdbfile)
 -  {
 -    return Color.white;
 -    // if (!pdbfile.equals(pdbentry.getFile()))
 -    // return null;
 -
 -    // return new Color(viewer.getAtomArgb(atomIndex));
 -  }
 -
 -  @Override
 -  public void updateColours(Object source)
 -  {
 -    colourBySequence();
 -    redrawneeded = true;
 -    repaint();
 -  }
 -
 -  @Override
 -  public void releaseReferences(Object svl)
 -  {
 -    // TODO Auto-generated method stub
 -
 -  }
+ 
 -  @Override
 -  public boolean isListeningFor(SequenceI seq)
 -  {
 -    if (sequence != null)
 -    {
 -      for (SequenceI s : sequence)
 -      {
 -        if (s == seq)
 -        {
 -          return true;
 -        }
 -      }
 -    }
 -    return false;
 -  }
+ }
diff --cc src/jalview/appletgui/EmbmenuFrame.java
index b6b81fa,7b489ea..0edb8c0
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@@ -51,8 -49,8 +51,9 @@@ import java.util.Map
   * @author Jim Procter and Andrew Waterhouse
   * 
   */
 +@SuppressWarnings("serial")
- public class EmbmenuFrame extends Frame implements MouseListener
+ public class EmbmenuFrame extends Frame
+         implements MouseListener, AutoCloseable
  {
    protected static final Font FONT_ARIAL_PLAIN_11 = new Font("Arial",
            Font.PLAIN, 11);
diff --cc src/jalview/appletgui/OverviewPanel.java
index 4e69399,8f72260..ddb49f1
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@@ -142,10 -140,10 +142,10 @@@ public class OverviewPanel extends Pane
    @Override
    public void mousePressed(MouseEvent evt)
    {
-     if ((evt.getModifiers()
-             & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+     if ((evt.getModifiersEx()
+             & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
      {
 -      if (!Platform.isAMac())
 +      if (!Platform.isMac()) // BH was excluding JavaScript
        {
          showPopupMenu(evt);
        }
@@@ -187,32 -185,32 +187,36 @@@
    @Override
    public void mouseDragged(MouseEvent evt)
    {
-     if (Platform.isWinRightButton(evt)) 
 -    if ((evt.getModifiersEx()
 -            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
++    if (Platform.isWinRightButton(evt))
      {
-     	showPopupMenu(evt);
-     	return;
 -      if (!Platform.isAMac())
++      if ((evt.getModifiersEx()
++              & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+       {
 -        showPopupMenu(evt);
++      	showPopupMenu(evt);
++      	return;
+       }
      }
 -    else
 -    {
 -      if (draggingBox)
 -      {
 -        // set the mouse position as a fixed point in the box
 -        // and drag relative to that position
 -        od.adjustViewportFromMouse(evt.getX(), evt.getY(),
 -                av.getAlignment().getHiddenSequences(),
 -                av.getAlignment().getHiddenColumns());
 -      }
 -      else
 -      {
 -        od.updateViewportFromMouse(evt.getX(), evt.getY(),
 -                av.getAlignment().getHiddenSequences(),
 -                av.getAlignment().getHiddenColumns());
 -      }
 -      ap.paintAlignment(false, false);
 +
 +    if (SwingUtilities.isRightMouseButton(evt))
 +    { 
 +    	return;
      }
 +    
 +	  if (draggingBox)
 +	  {
 +	    // set the mouse position as a fixed point in the box
 +	    // and drag relative to that position
 +	    od.adjustViewportFromMouse(evt.getX(), evt.getY(),
 +	            av.getAlignment().getHiddenSequences(),
 +	            av.getAlignment().getHiddenColumns());
 +	  }
 +	  else
 +	  {
 +	    od.updateViewportFromMouse(evt.getX(), evt.getY(),
 +	            av.getAlignment().getHiddenSequences(),
 +	            av.getAlignment().getHiddenColumns());
 +	  }
 +	  ap.paintAlignment(false, false);
    }
  
    /**
diff --cc src/jalview/appletgui/SeqPanel.java
index 32f0abb,fee68c8..5becbc1
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@@ -500,8 -499,9 +500,7 @@@ public class SeqPanel extends Panel imp
  
      // For now, ignore the mouseWheel font resizing on Macs
      // As the Button2_mask always seems to be true
-     
 -    if ((evt.getModifiersEx()
 -            & InputEvent.BUTTON2_DOWN_MASK) == InputEvent.BUTTON2_DOWN_MASK
 -            && !av.MAC)
 +    if (Platform.isWinMiddleButton(evt))
      {
        mouseWheelPressed = true;
        return;
diff --cc src/jalview/bin/Jalview.java
index 694fe00,c66e63e..b245cf4
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@@ -406,30 -352,42 +425,42 @@@ public class Jalvie
  
      if (!headless)
      {
 -      desktop = new Desktop();
 +      desktop = new Desktop() 
 +//      {
 +// // BH testing
 +//    	  @Override
 +//    	  protected void processEvent(AWTEvent e) {
 +//    		  System.out.println("Jalview.java " + e);
 +//    		  super.processEvent(e);
 +//    	  }
 +//       }
 +      ;
        desktop.setInBatchMode(true); // indicate we are starting up
+ 
+       try
+       {
+         JalviewTaskbar.setTaskbar(this);
+       } catch (Exception e)
+       {
+         e.printStackTrace();
+       } catch (Throwable t)
+       {
+         t.printStackTrace();
+       }
+ 
        desktop.setVisible(true);
 -      desktop.startServiceDiscovery();
 -      if (!aparser.contains("nousagestats"))
 -      {
 -        startUsageStats(desktop);
 -      }
 -      else
 -      {
 -        System.err.println("CMD [-nousagestats] executed successfully!");
 -      }
  
 -      if (!aparser.contains("noquestionnaire"))
 +      if (!Platform.isJS())
 +      /**
 +       * Java only
 +       * 
 +       * @j2sIgnore
 +       */
        {
 -        String url = aparser.getValue("questionnaire");
 -        if (url != null)
 +        desktop.startServiceDiscovery();
 +        if (!aparser.contains("nousagestats"))
          {
 -          // Start the desktop questionnaire prompter with the specified
 -          // questionnaire
 -          Cache.log.debug("Starting questionnaire url at " + url);
 -          desktop.checkForQuestionnaire(url);
 -          System.out.println(
 -                  "CMD questionnaire[-" + url + "] executed successfully!");
 +          startUsageStats(desktop);
          }
          else
          {
diff --cc src/jalview/ext/ensembl/EnsemblMap.java
index add71b3,b1c9d86..e9f1af1
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@@ -14,10 -13,24 +14,22 @@@ import java.util.ArrayList
  import java.util.Collections;
  import java.util.Iterator;
  import java.util.List;
 +import java.util.Map;
  
 -import org.json.simple.JSONArray;
 -import org.json.simple.JSONObject;
 -import org.json.simple.parser.JSONParser;
  import org.json.simple.parser.ParseException;
  
+ /**
+  * A client for the Ensembl REST service /map endpoint, to convert from
+  * coordinates of one genome assembly to another.
+  * <p>
+  * Note that species and assembly identifiers passed to this class must be valid
+  * in Ensembl. They are not case sensitive.
+  * 
+  * @author gmcarstairs
+  * @see https://rest.ensembl.org/documentation/info/assembly_map
+  * @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
+  * @see https://rest.ensembl.org/info/species?content-type=text/xml
+  */
  public class EnsemblMap extends EnsemblRestClient
  {
    private static final String MAPPED = "mapped";
diff --cc src/jalview/ext/paradise/Annotate3D.java
index 3b7044b,b8ba847..3c443de
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@@ -159,84 -154,19 +159,17 @@@ public class Annotate3
    public static Iterator<Reader> processJsonResponseFor(Reader respons)
            throws Exception
    {
- 	  // BH 2019 never called?
 -    org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
      try
      {
 -      final JSONArray responses = (JSONArray) jp.parse(respons);
 -      final RvalsIterator rvals = new RvalsIterator(responses);
 -      return rvals;
 +      @SuppressWarnings("unchecked")
- 	final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
-       return new Iterator<Reader>()
-       {
-         @Override
-         public boolean hasNext()
-         {
-           return rvals.hasNext();
-         }
- 
-         @SuppressWarnings("unchecked")
- 		@Override
-         public Reader next()
-         {
-           Map<String, Object> val = (Map<String, Object>) rvals.next();
- 
-           Object sval = null;
-           try
-           {
-             sval = val.get("2D");
-           } catch (Exception x)
-           {
-             x.printStackTrace();
-           }
-           ;
-           if (sval == null)
-           {
-             System.err.println(
-                     "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
-                             + val.toString());
- 
-             sval = "";
-           }
-           return new StringReader(sval.toString());
- 
-         }
- 
-         @Override
-         public void remove()
-         {
-           throw new Error(
-                   MessageManager.getString("error.not_implemented_remove"));
- 
-         }
- 
-         @Override
-         protected Object clone() throws CloneNotSupportedException
-         {
-           throw new CloneNotSupportedException(
-                   MessageManager.getString("error.not_implemented_clone"));
-         }
- 
-         @Override
-         public boolean equals(Object obj)
-         {
-           return super.equals(obj);
-         }
- 
-         @Override
-         protected void finalize() throws Throwable
-         {
-           while (rvals.hasNext())
-           {
-             rvals.next();
-           }
-           super.finalize();
-         }
-       };
++	List<Object> responses = (List<Object>) JSONUtils.parse(respons);
++      return new RvalsIterator(responses);
      } catch (Exception foo)
      {
        throw new Exception(MessageManager.getString(
                "exception.couldnt_parse_responde_from_annotated3d_server"),
                foo);
      }
--
    }
  
    public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
@@@ -256,3 -186,77 +189,64 @@@
    }
  
  }
+ 
 -class RvalsIterator implements Iterator, AutoCloseable
++class RvalsIterator implements Iterator<Reader>, AutoCloseable
+ {
 -  private Iterator rvals;
++  private Iterator<Object> rvals;
+ 
 -  protected RvalsIterator(JSONArray responses)
++  protected RvalsIterator(List<Object> responses)
+   {
+     this.rvals = responses.iterator();
+   }
+ 
+   @Override
+   public boolean hasNext()
+   {
+     return rvals.hasNext();
+   }
+ 
+   @Override
+   public Reader next()
+   {
 -    JSONObject val = (JSONObject) rvals.next();
++    Map<String, Object> val = (Map<String, Object>) rvals.next();
+ 
+     Object sval = null;
+     try
+     {
+       sval = val.get("2D");
+     } catch (Exception x)
+     {
+       x.printStackTrace();
+     }
 -    ;
+     if (sval == null)
+     {
+       System.err.println(
+               "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+                       + val.toString());
+ 
+       sval = "";
+     }
 -    return new StringReader(
 -            (sval instanceof JSONObject) ? ((JSONObject) sval).toString()
 -                    : sval.toString());
 -
++    return new StringReader(sval.toString());
+   }
+ 
+   @Override
+   public void remove()
+   {
 -    throw new Error(
 -            MessageManager.getString("error.not_implemented_remove"));
 -
++    throw new UnsupportedOperationException();
+   }
+ 
+   @Override
+   protected Object clone() throws CloneNotSupportedException
+   {
 -    throw new CloneNotSupportedException(
 -            MessageManager.getString("error.not_implemented_clone"));
 -  }
 -
 -  @Override
 -  public boolean equals(Object obj)
 -  {
 -    return super.equals(obj);
++    throw new UnsupportedOperationException();
+   }
+ 
+   @Override
+   public void close()
+   {
+     while (rvals.hasNext())
+     {
+       rvals.next();
+     }
+   }
+ }
diff --cc src/jalview/gui/APQHandlers.java
index 0000000,31f7a6d..3706cba
mode 000000,100644..100644
--- a/src/jalview/gui/APQHandlers.java
+++ b/src/jalview/gui/APQHandlers.java
@@@ -1,0 -1,150 +1,150 @@@
+ package jalview.gui;
+ 
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+ 
+ import java.awt.Desktop;
+ import java.awt.desktop.AboutEvent;
+ import java.awt.desktop.AboutHandler;
+ import java.awt.desktop.PreferencesEvent;
+ import java.awt.desktop.PreferencesHandler;
+ import java.awt.desktop.QuitEvent;
+ import java.awt.desktop.QuitHandler;
+ import java.awt.desktop.QuitResponse;
+ import java.awt.desktop.QuitStrategy;
+ 
+ import javax.swing.JOptionPane;
+ 
+ public class APQHandlers
+ {
+   private static boolean setAPQHandlers = false;
+ 
+   public APQHandlers() {
+   }
+ 
+   protected static boolean setAPQHandlers(jalview.gui.Desktop jalviewDesktop)
+   {
+     // flagging this test to avoid unnecessary reflection
+     if (!setAPQHandlers)
+     {
+       // see if the Quit, About and Preferences handlers are available
+       Class desktopClass = Desktop.class;
+       Desktop hdesktop = Desktop.getDesktop();
+ 
+       try
+       {
+         Float specversion = Float.parseFloat(
+                 System.getProperty("java.specification.version"));
+ 
+         if (specversion >= 9)
+         {
 -          if (Platform.isAMac())
++          if (Platform.isMac())
+           {
+             if (desktopClass.getDeclaredMethod("setAboutHandler",
+                     new Class[]
+                     { AboutHandler.class }) != null)
+             {
+ 
+               hdesktop.setAboutHandler(new AboutHandler()
+               {
+                 @Override
+                 public void handleAbout(AboutEvent e)
+                 {
+                   jalviewDesktop.aboutMenuItem_actionPerformed(null);
+                 }
+               });
+ 
+             }
+ 
+             if (desktopClass.getDeclaredMethod("setPreferencesHandler",
+                     new Class[]
+                     { PreferencesHandler.class }) != null)
+             {
+ 
+               hdesktop.setPreferencesHandler(
+                       new PreferencesHandler()
+               {
+                         @Override
+                         public void handlePreferences(
+                                 PreferencesEvent e)
+                         {
+                           jalviewDesktop.preferences_actionPerformed(null);
+                         }
+                       });
+ 
+             }
+ 
+             if (desktopClass.getDeclaredMethod("setQuitHandler",
+                     new Class[]
+                     { QuitHandler.class }) != null)
+             {
+ 
+               hdesktop.setQuitHandler(new QuitHandler()
+               {
+                 @Override
+                 public void handleQuitRequestWith(
+                         QuitEvent e, QuitResponse r)
+                 {
+                   boolean confirmQuit = jalview.bin.Cache
+                           .getDefault(jalviewDesktop.CONFIRM_KEYBOARD_QUIT,
+                                   true);
+                   int n;
+                   if (confirmQuit)
+                   {
+                     n = JOptionPane.showConfirmDialog(null,
+                             MessageManager.getString("label.quit_jalview"),
+                             MessageManager.getString("action.quit"),
+                             JOptionPane.OK_CANCEL_OPTION,
+                             JOptionPane.PLAIN_MESSAGE, null);
+                   }
+                   else
+                   {
+                     n = JOptionPane.OK_OPTION;
+                   }
+                   if (n == JOptionPane.OK_OPTION)
+                   {
+                     System.out.println("Shortcut Quit confirmed by user");
+                     jalviewDesktop.quit();
+                     r.performQuit(); // probably won't reach this line, but just
+                                      // in
+                                      // case
+                   }
+                   else
+                   {
+                     r.cancelQuit();
+                     System.out.println("Shortcut Quit cancelled by user");
+                   }
+                 }
+               });
+               hdesktop.setQuitStrategy(
+                       QuitStrategy.CLOSE_ALL_WINDOWS);
+ 
+             }
+           }
+           setAPQHandlers = true;
+         }
+         else
+         {
+           System.out.println(
+                   "Not going to try setting APQ Handlers as java.spec.version is "
+                           + specversion);
+         }
+ 
+       } catch (Exception e)
+       {
+         System.out.println(
+                 "Exception when looking for About, Preferences, Quit Handlers");
+         e.printStackTrace();
+       } catch (Throwable t)
+       {
+         System.out.println(
+                 "Throwable when looking for About, Preferences, Quit Handlers");
+         t.printStackTrace();
+       }
+ 
+     }
+     
+     return setAPQHandlers;
+   }
+ 
+ }
diff --cc src/jalview/gui/AlignFrame.java
index 27a0f76,0ab7515..1b09868
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1249,80 -1168,94 +1249,79 @@@ public class AlignFrame extends GAlignF
        statusBar.setText(MessageManager.formatMessage(
                "label.successfully_saved_to_file_in_format", new Object[]
                { fileName, format }));
 -
 +      
 +      return;
      }
 -    else
 +
 +    AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
 +    Runnable cancelAction = new Runnable()
      {
 -      AlignmentExportData exportData = getAlignmentForExport(format,
 -              viewport, null);
 -      if (exportData.getSettings().isCancelled())
 -      {
 -        return false;
 -      }
 -      FormatAdapter f = new FormatAdapter(alignPanel,
 -              exportData.getSettings());
 -      String output = f.formatSequences(format, exportData.getAlignment(), // class
 -                                                                           // cast
 -                                                                           // exceptions
 -                                                                           // will
 -              // occur in the distant future
 -              exportData.getOmitHidden(), exportData.getStartEndPostions(),
 -              f.getCacheSuffixDefault(format),
 -              viewport.getAlignment().getHiddenColumns());
 -
 -      if (output == null)
 +      @Override
 +      public void run()
        {
 -        success = false;
 +        lastSaveSuccessful = false;
        }
 -      else
 +    };
 +    Runnable outputAction = new Runnable()
 +    {
 +      @Override
 +      public void run()
        {
 -        // create backupfiles object and get new temp filename destination
 -        BackupFiles backupfiles = new BackupFiles(file);
 -
 -        try
 +        // todo defer this to inside formatSequences (or later)
 +        AlignmentExportData exportData = viewport
 +                .getAlignExportData(options);
 +        String output = new FormatAdapter(alignPanel, options)
 +                .formatSequences(format, exportData.getAlignment(),
 +                        exportData.getOmitHidden(),
 +                        exportData.getStartEndPostions(),
 +                        viewport.getAlignment().getHiddenColumns());
 +        if (output == null)
          {
 -          PrintWriter out = new PrintWriter(
 -                  new FileWriter(backupfiles.getTempFilePath()));
 -
 -          // TESTING code here
 -          boolean TESTING = true;
 -          if (TESTING)
 +          lastSaveSuccessful = false;
 +        }
 +        else
 +        {
 +          // create backupfiles object and get new temp filename destination
 +          boolean doBackup = BackupFiles.getEnabled();
 +          BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
 +          try
            {
 -            out.print("; TESTSTART\n");
 -            int count = 20;
 -            for (int i = 0; i < count; i++)
 -            {
 -              // Thread.sleep(1000);
 -              out.println("; TEST: " + (count - 1 - i));
 -            }
 +            String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
 +			PrintWriter out = new PrintWriter(
 +                    new FileWriter(tempFilePath));
- 
 +            out.print(output);
 +            out.close();
 +            AlignFrame.this.setTitle(file);
 +            statusBar.setText(MessageManager.formatMessage(
 +                  "label.successfully_saved_to_file_in_format", new Object[]
 +                  { fileName, format.getName() }));
 +            lastSaveSuccessful = true;
 +          } catch (Exception ex)
 +          {
 +            lastSaveSuccessful = false;
 +            ex.printStackTrace();
            }
 -          out.print(output);
 -          if (TESTING)
 +
 +          if (doBackup)
            {
 -            out.print("; TESTEND\n");
 +            backupfiles.setWriteSuccess(lastSaveSuccessful);
 +            // do the backup file roll and rename the temp file to actual file
 +            lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
            }
 -          out.close();
 -          this.setTitle(file);
 -          statusBar.setText(MessageManager.formatMessage(
 -                  "label.successfully_saved_to_file_in_format", new Object[]
 -                  { fileName, format.getName() }));
 -        } catch (Exception ex)
 -        {
 -          success = false;
 -          ex.printStackTrace();
          }
 -
 -        backupfiles.setWriteSuccess(success);
 -        // do the backup file roll and rename the temp file to actual file
 -        success = backupfiles.rollBackupsAndRenameTempFile();
 -
        }
 -    }
 -
 -    if (!success)
 -    {
 -      JvOptionPane.showInternalMessageDialog(this, MessageManager
 -              .formatMessage("label.couldnt_save_file", new Object[]
 -              { fileName }),
 -              MessageManager.getString("label.error_saving_file"),
 -              JvOptionPane.WARNING_MESSAGE);
 -    }
 +    };
  
 -    return success;
 -  }
 -
 -  private void warningMessage(String warning, String title)
 -  {
 -    if (new jalview.util.Platform().isHeadless())
 +    /*
 +     * show dialog with export options if applicable; else just do it
 +     */
 +    if (AlignExportOptions.isNeeded(viewport, format))
      {
 -      System.err.println("Warning: " + title + "\nWarning: " + warning);
 -
 +      AlignExportOptions choices = new AlignExportOptions(
 +              alignPanel.getAlignViewport(), format, options);
 +      choices.setResponseAction(0, outputAction);
 +      choices.setResponseAction(1, cancelAction);
 +      choices.showDialog();
      }
      else
      {
diff --cc src/jalview/gui/Desktop.java
index cd8330a,41cbad8..e6d7a15
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@@ -366,9 -391,9 +404,10 @@@ public class Desktop extends jalview.jb
      boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
              false);
      desktop = new MyDesktopPane(selmemusage);
 +
      showMemusage.setSelected(selmemusage);
      desktop.setBackground(Color.white);
+ 
      getContentPane().setLayout(new BorderLayout());
      // alternate config - have scrollbars - see notes in JAL-153
      // JScrollPane sp = new JScrollPane();
@@@ -401,86 -419,41 +440,92 @@@
      else
      {
        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
 -      setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
 -              900, 650);
 -    }
 -    jconsole = new Console(this, showjconsole);
 -    // add essential build information
 -    jconsole.setHeader(
 -            "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
 -                    + "\n" + "Jalview Installation: "
 -                    + jalview.bin.Cache.getDefault("INSTALLATION",
 -                            "unknown")
 -                    + "\n" + "Build Date: "
 -                    + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
 -                    + "\n" + "Java version: "
 -                    + System.getProperty("java.version") + "\n"
 -                    + System.getProperty("os.arch") + " "
 -                    + System.getProperty("os.name") + " "
 -                    + System.getProperty("os.version")
 -                    + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
 -                                    ? "\nJava path:"
 -                                            + System.getProperty(
 -                                                    "java.home")
 -                                            + File.separator + "bin"
 -                                            + File.separator + "java"
 -                                    : "")
 -            );
 -
 -    showConsole(showjconsole);
 -
 -    showNews.setVisible(false);
 -
 -    experimentalFeatures.setSelected(showExperimental());
 -
 -    getIdentifiersOrgData();
 -
 -    checkURLLinks();
 +      int xPos = Math.max(5, (screenSize.width - 900) / 2);
 +      int yPos = Math.max(5, (screenSize.height - 650) / 2);
 +      setBounds(xPos, yPos, 900, 650);
 +    }
 +
 +    if (!Platform.isJS())
 +    /**
 +     * Java only
 +     * 
 +     * @j2sIgnore
 +     */
 +    {
 +
 +      jconsole = new Console(this, showjconsole);
 +      // add essential build information
 +      jconsole.setHeader("Jalview Version: "
 +              + jalview.bin.Cache.getProperty("VERSION") + "\n"
 +              + "Jalview Installation: "
 +              + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
 +              + "\n" + "Build Date: "
 +              + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
 +              + "Java version: " + System.getProperty("java.version") + "\n"
 +              + System.getProperty("os.arch") + " "
 +              + System.getProperty("os.name") + " "
-               + System.getProperty("os.version"));
++              + System.getProperty("os.version")
++              + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
++                              ? "\nJava path:"
++                                      + System.getProperty(
++                                              "java.home")
++                                      + File.separator + "bin"
++                                      + File.separator + "java"
++                              : ""));
 +
 +      showConsole(showjconsole);
 +
 +      showNews.setVisible(false);
 +
 +      experimentalFeatures.setSelected(showExperimental());
 +
 +      getIdentifiersOrgData();
 +
 +      checkURLLinks();
 +
 +      // Spawn a thread that shows the splashscreen
 +
 +      SwingUtilities.invokeLater(new Runnable()
 +      {
 +        @Override
 +        public void run()
 +        {
 +          new SplashScreen();
 +        }
 +      });
 +
 +      // Thread off a new instance of the file chooser - this reduces the time
-       // it
-       // takes to open it later on.
++      // it takes to open it later on.
 +      new Thread(new Runnable()
 +      {
 +        @Override
 +        public void run()
 +        {
 +          Cache.log.debug("Filechooser init thread started.");
 +          String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 +          JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
 +                  fileFormat);
 +          Cache.log.debug("Filechooser init thread finished.");
 +        }
 +      }).start();
 +      // Add the service change listener
 +      changeSupport.addJalviewPropertyChangeListener("services",
 +              new PropertyChangeListener()
 +              {
 +
 +                @Override
 +                public void propertyChange(PropertyChangeEvent evt)
 +                {
 +                  Cache.log.debug("Firing service changed event for "
 +                          + evt.getNewValue());
 +                  JalviewServicesChanged(evt);
 +                }
 +
 +              });
 +
 +    }
 +
 +    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
  
      this.addWindowListener(new WindowAdapter()
      {
@@@ -589,7 -602,7 +634,7 @@@
          }
        }
      }).start();
--    ;
++    
    }
  
    @Override
@@@ -940,7 -956,7 +985,7 @@@
            menuItem.removeActionListener(menuItem.getActionListeners()[0]);
          }
          windowMenu.remove(menuItem);
--      };
++      }
      });
  
      menuItem.addActionListener(new ActionListener()
@@@ -2342,7 -2317,7 +2389,7 @@@
                  });
                  rthr.start();
                }
--            };
++            }
            });
            VamsasStMenu.add(sessit);
          }
@@@ -3239,7 -3212,7 +3286,6 @@@
            } catch (InterruptedException x)
            {
            }
--          ;
          }
          if (instance == null)
          {
@@@ -3527,7 -3469,7 +3573,6 @@@
              System.err.println(
                      "Please ignore plist error - occurs due to problem with java 8 on OSX");
            }
--          ;
          }
        } catch (Throwable ex)
        {
diff --cc src/jalview/gui/FeatureTypeSettings.java
index 735e514,a2194f4..80861ac
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@@ -1443,11 -1419,9 +1443,12 @@@ public class FeatureTypeSettings extend
              || (pattern != null && pattern.trim().length() > 0))
      {
        JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
 +      removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
 +      removeCondition.setBackground(Color.WHITE);
 +      removeCondition.setPreferredSize(new Dimension(23, 17));
-       removeCondition
-               .setToolTipText(MessageManager.getString("label.delete_row"));
+       removeCondition.setToolTipText(
+               MessageManager.getString("label.delete_condition"));
+       removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
        removeCondition.addActionListener(new ActionListener()
        {
          @Override
diff --cc src/jalview/jbgui/GDesktop.java
index 2ea3774,fe85043..4e01b25
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@@ -452,18 -448,15 +453,18 @@@ public class GDesktop extends JFram
      VamsasMenu.add(vamsasImport);
      VamsasMenu.add(vamsasSave);
      VamsasMenu.add(vamsasStop);
-     toolsMenu.add(preferences);
-     if (!Platform.isJS())
 -    if (!Platform.isAMac() || specversion < 11)
++    if (!Platform.isMac() || specversion < 11)
      {
-       toolsMenu.add(showMemusage);
-       toolsMenu.add(showConsole);
+       toolsMenu.add(preferences);
      }
 -    toolsMenu.add(showMemusage);
 -    toolsMenu.add(showConsole);
 -    toolsMenu.add(showNews);
 -    toolsMenu.add(garbageCollect);
 -    toolsMenu.add(groovyShell);
 +    if (!Platform.isJS())
 +    {
++      toolsMenu.add(showMemusage);
++      toolsMenu.add(showConsole);
 +      toolsMenu.add(showNews);
 +      toolsMenu.add(garbageCollect);
 +      toolsMenu.add(groovyShell);
 +    }
      toolsMenu.add(experimentalFeatures);
      // toolsMenu.add(snapShotWindow);
      inputMenu.add(inputLocalFileMenuItem);
diff --cc src/jalview/project/Jalview2XML.java
index 4d772a1,0d2ec68..5618529
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@@ -1672,7 -1659,6 +1672,7 @@@ public class Jalview2XM
        // using save and then load
        try
        {
-     	fileName = fileName.replace('\\', '/');
++        fileName = fileName.replace('\\', '/');
          System.out.println("Writing jar entry " + fileName);
          JarEntry entry = new JarEntry(fileName);
          jout.putNextEntry(entry);
@@@ -2771,52 -2755,44 +2771,52 @@@
      return af;
    }
  
- 	@SuppressWarnings("unused")
- 	private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
 -  private jarInputStreamProvider createjarInputStreamProvider(
 -          final String file) throws MalformedURLException
 -  {
 -    URL url = null;
 -    errorMessage = null;
 -    uniqueSetSuffix = null;
 -    seqRefIds = null;
 -    viewportsAdded.clear();
 -    frefedSequence = null;
 -
 -    if (file.startsWith("http://"))
 -    {
 -      url = new URL(file);
 -    }
 -    final URL _url = url;
 -    return new jarInputStreamProvider()
 -    {
 -
 -      @Override
 -      public JarInputStream getJarInputStream() throws IOException
 -      {
 -        if (_url != null)
 -        {
 -          return new JarInputStream(_url.openStream());
 -        }
 -        else
 -        {
 -          return new JarInputStream(new FileInputStream(file));
++        @SuppressWarnings("unused")
++        private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
 +
- 		// BH 2018 allow for bytes already attached to File object
- 		try {
- 			String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
++                // BH 2018 allow for bytes already attached to File object
++                try {
++                        String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
 +      byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
 +              : null;
- 			URL url = null;
- 			errorMessage = null;
- 			uniqueSetSuffix = null;
- 			seqRefIds = null;
- 			viewportsAdded.clear();
- 			frefedSequence = null;
- 
- 			if (file.startsWith("http://")) {
- 				url = new URL(file);
- 			}
- 			final URL _url = url;
- 			return new jarInputStreamProvider() {
- 
- 				@Override
- 				public JarInputStream getJarInputStream() throws IOException {
- 					if (bytes != null) {
- //						System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
- 						return new JarInputStream(new ByteArrayInputStream(bytes));
- 					}
- 					if (_url != null) {
- //						System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
- 						return new JarInputStream(_url.openStream());
- 					} else {
- //						System.out.println("Jalview2XML: opening file jarInputStream for " + file);
- 						return new JarInputStream(new FileInputStream(file));
- 					}
- 				}
- 
- 				@Override
- 				public String getFilename() {
- 					return file;
- 				}
- 			};
- 		} catch (IOException e) {
- 			e.printStackTrace();
- 			return null;
- 		}
- 	}
++                        URL url = null;
++                        errorMessage = null;
++                        uniqueSetSuffix = null;
++                        seqRefIds = null;
++                        viewportsAdded.clear();
++                        frefedSequence = null;
++
++                        if (file.startsWith("http://")) {
++                                url = new URL(file);
++                        }
++                        final URL _url = url;
++                        return new jarInputStreamProvider() {
++
++                                @Override
++                                public JarInputStream getJarInputStream() throws IOException {
++                                        if (bytes != null) {
++//                                              System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
++                                                return new JarInputStream(new ByteArrayInputStream(bytes));
++                                        }
++                                        if (_url != null) {
++//                                              System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
++                                                return new JarInputStream(_url.openStream());
++                                        } else {
++//                                              System.out.println("Jalview2XML: opening file jarInputStream for " + file);
++                                                return new JarInputStream(new FileInputStream(file));
++                                        }
++                                }
++
++                                @Override
++                                public String getFilename() {
++                                        return file;
++                                }
++                        };
++                } catch (IOException e) {
++                        e.printStackTrace();
++                        return null;
++                }
+         }
 -      }
 -
 -      @Override
 -      public String getFilename()
 -      {
 -        return file;
 -      }
 -    };
 -  }
  
    /**
     * Recover jalview session from a jalview project archive. Caller may
@@@ -4855,18 -4839,7 +4855,18 @@@
    {
      AlignFrame af = null;
      af = new AlignFrame(al, safeInt(view.getWidth()),
 -            safeInt(view.getHeight()), uniqueSeqSetId, viewId);
 +            safeInt(view.getHeight()), uniqueSeqSetId, viewId) 
 +//    {
- //    	
- //    	@Override
- //    	protected void processKeyEvent(java.awt.event.KeyEvent e) {
- //    		System.out.println("Jalview2XML   AF " + e);
- //    		super.processKeyEvent(e);
- //    		
- //    	}
- //    	
++//      
++//      @Override
++//      protected void processKeyEvent(java.awt.event.KeyEvent e) {
++//              System.out.println("Jalview2XML   AF " + e);
++//              super.processKeyEvent(e);
++//              
++//      }
++//      
 +//    }
 +    ;
  
      af.setFileName(file, FileFormat.Jalview);
  
diff --cc src/jalview/util/Platform.java
index f9eb2a6,c1d8228..bf0dfcd
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@@ -177,438 -122,41 +169,463 @@@ public class Platfor
     */
    protected static boolean isControlDown(MouseEvent e, boolean aMac)
    {
-     if (!aMac)
-     {
-       return e.isControlDown();
-     }
-     // answer false for right mouse button
-     // shortcut key will be META for a Mac
-     return !e.isPopupTrigger()
-             && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                     & e.getModifiers()) != 0;
-     // could we use e.isMetaDown() here?
-   }
 -    if (aMac)
++	    if (aMac)
++	    {
++	      /*
++	       * answer false for right mouse button
++	       */
++	      if (e.isPopupTrigger())
++	      {
++	        return false;
++	      }
++	      return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
++	              & e.getModifiersEx()) != 0; // getModifiers()) != 0;
++	    }
++	    return e.isControlDown();
++	  }
 +
 +  // BH: I don't know about that previous method. Here is what SwingJS uses.
 +  // Notice the distinction in mouse events. (BUTTON3_MASK == META)
 +  //
 +  // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
 +  // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
 +  // if (isWin) {
 +  // if (id != MouseEvent.MOUSE_RELEASED)
 +  // return false;
 +  ////
 +  //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
 +  //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
 +  ////
 +  //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
 +  // because
 +  //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
 +  ////
 +  // return rt;
 +  // } else {
 +  // // mac, linux, unix
 +  // if (id != MouseEvent.MOUSE_PRESSED)
 +  // return false;
 +  // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
 +  // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
 +  // return rt || (ctrl && lt);
 +  // }
 +  // }
 +  //
 +
 +  /**
 +   * Windows (not Mac, Linux, or Unix) and right button to test for the
 +   * right-mouse pressed event in Windows that would have opened a menu or a
 +   * Mac.
 +   * 
 +   * @param e
 +   * @return
 +   */
 +  public static boolean isWinRightButton(MouseEvent e)
 +  {
 +    // was !isAMac(), but that is true also for Linux and Unix and JS,
 +
 +    return isWin() && SwingUtilities.isRightMouseButton(e);
 +  }
 +
 +  /**
 +   * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
 +   * without pressing the button.
 +   * 
 +   * @param e
 +   * @return
 +   */
 +  public static boolean isWinMiddleButton(MouseEvent e)
 +  {
 +    // was !isAMac(), but that is true also for Linux and Unix and JS
 +    return isWin() && SwingUtilities.isMiddleMouseButton(e);
 +  }
 +
 +  public static boolean allowMnemonics()
 +  {
 +    return !isMac();
 +  }
 +
 +  public final static int TIME_RESET = 0;
 +
 +  public final static int TIME_MARK = 1;
 +
 +  public static final int TIME_SET = 2;
 +
 +  public static final int TIME_GET = 3;
 +
 +  public static long time, mark, set, duration;
 +
 +  public static void timeCheck(String msg, int mode)
 +  {
 +    long t = System.currentTimeMillis();
 +    switch (mode)
      {
 -      /*
 -       * answer false for right mouse button
 -       */
 -      if (e.isPopupTrigger())
 +    case TIME_RESET:
 +      time = mark = t;
 +      if (msg != null)
 +      {
 +        System.err.println("Platform: timer reset\t\t\t" + msg);
 +      }
 +      break;
 +    case TIME_MARK:
 +      if (set > 0)
 +      {
 +        duration += (t - set);
 +      }
 +      else
        {
 -        return false;
 +        if (time == 0)
 +        {
 +          time = mark = t;
 +        }
 +        if (msg != null)
 +        {
 +          System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
 +                  + "\t" + ((t - mark) / 1000f) + "\t" + msg);
 +        }
 +        mark = t;
        }
 -      return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
 -              & e.getModifiersEx()) != 0; // getModifiers()) != 0;
 +      break;
 +    case TIME_SET:
 +      set = t;
 +      break;
 +    case TIME_GET:
 +      if (msg != null)
 +      {
 +        System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
 +                + "\t" + ((duration) / 1000f) + "\t" + msg);
 +      }
 +      set = 0;
 +      break;
      }
 -    return e.isControlDown();
 +  }
 +
 +  public static void cacheFileData(String path, Object data)
 +  {
 +    if (!isJS() || data == null)
 +    {
 +      return;
 +    }
 +    /**
 +     * @j2sNative
 +     * 
 +     *            swingjs.JSUtil.cacheFileData$S$O(path, data);
 +     * 
 +     */
 +  }
 +
 +  public static void cacheFileData(File file)
 +  {
 +    byte[] data;
 +    if (!isJS() || (data = Platform.getFileBytes(file)) == null)
 +    {
 +      return;
 +    }
 +    cacheFileData(file.toString(), data);
 +  }
 +
 +  public static byte[] getFileBytes(File f)
 +  {
 +    return /** @j2sNative f && f._bytes || */
 +    null;
 +  }
 +
 +  public static byte[] getFileAsBytes(String fileStr)
 +  {
 +    byte[] bytes = null;
 +    // BH 2018 hack for no support for access-origin
 +    /**
 +     * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
 +     */
 +    cacheFileData(fileStr, bytes);
 +    return bytes;
 +  }
 +
 +  @SuppressWarnings("unused")
 +  public static String getFileAsString(String url)
 +  {
 +    String ret = null;
 +    /**
 +     * @j2sNative
 +     * 
 +     *            ret = swingjs.JSUtil.getFileAsString$S(url);
 +     * 
 +     * 
 +     */
 +    cacheFileData(url, ret);
 +    return ret;
 +  }
 +
 +  public static boolean setFileBytes(File f, String urlstring)
 +  {
 +    if (!isJS())
 +    {
 +      return false;
 +    }
 +    @SuppressWarnings("unused")
 +    byte[] bytes = getFileAsBytes(urlstring);
 +    /**
 +     * @j2sNative f._bytes = bytes;
 +     */
 +    return true;
 +  }
 +
 +  public static void addJ2SBinaryType(String ext)
 +  {
 +    /**
 +     * @j2sNative
 +     * 
 +     *            J2S._binaryTypes.push("." + ext + "?");
 +     * 
 +     */
 +  }
 +
 +  /**
 +   * Encode the URI using JavaScript encodeURIComponent
 +   * 
 +   * @param value
 +   * @return encoded value
 +   */
 +  public static String encodeURI(String value)
 +  {
 +    /**
 +     * @j2sNative value = encodeURIComponent(value);
 +     */
 +    return value;
 +  }
 +
 +  /**
 +   * Open the URL using a simple window call if this is JavaScript
 +   * 
 +   * @param url
 +   * @return true if window has been opened
 +   */
 +  public static boolean openURL(String url)
 +  {
 +    if (!isJS())
 +    {
 +      return false;
 +    }
 +    /**
 +     * @j2sNative
 +     * 
 +     * 
 +     *            window.open(url);
 +     */
 +    return true;
 +  }
 +
 +  public static String getUniqueAppletID()
 +  {
 +    @SuppressWarnings("unused")
 +    ThreadGroup g = Thread.currentThread().getThreadGroup();
 +    /**
 +     * @j2sNative return g.html5Applet._uniqueId;
 +     *
 +     */
 +    return null;
 +
 +  }
 +
 +  /**
 +   * Read the Info block for this applet.
 +   * 
 +   * @param prefix
 +   *          "jalview_"
 +   * @param p
 +   * @return unique id for this applet
 +   */
 +  public static void readInfoProperties(String prefix, Properties p)
 +  {
 +    if (!isJS())
 +    {
 +      return;
 +    }
 +    @SuppressWarnings("unused")
 +    ThreadGroup g = Thread.currentThread().getThreadGroup();
 +    String id = getUniqueAppletID();
 +    String key = "", value = "";
 +    /**
 +     * @j2sNative var info = g.html5Applet.__Info || {}; for (var key in info) {
 +     *            if (key.indexOf(prefix) == 0) { value = "" + info[key];
 +     */
 +
 +    System.out.println(
 +            "Platform id=" + id + " reading Info." + key + " = " + value);
 +    p.put(id + "_" + key, value);
 +
 +    /**
 +     * @j2sNative
 +     * 
 +     * 
 +     *            } }
 +     */
 +  }
 +
 +  public static void setAjaxJSON(URL url)
 +  {
 +    if (isJS())
 +    {
 +      JSON.setAjax(url);
 +    }
 +  }
 +
 +  public static Object parseJSON(InputStream response)
 +          throws IOException, ParseException
 +  {
 +    if (isJS())
 +    {
 +      return JSON.parse(response);
 +    }
 +
 +    BufferedReader br = null;
 +    try
 +    {
 +      br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
 +      return new JSONParser().parse(br);
 +    } finally
 +    {
 +      if (br != null)
 +      {
 +        try
 +        {
 +          br.close();
 +        } catch (IOException e)
 +        {
 +          // ignore
 +        }
 +      }
 +    }
 +  }
 +
 +  public static Object parseJSON(String json) throws ParseException
 +  {
 +    return (isJS() ? JSON.parse(json)
 +            : new JSONParser().parse(json));
 +  }
 +
 +  public static Object parseJSON(Reader r)
 +          throws IOException, ParseException
 +  {
 +    if (r == null)
 +    {
 +      return null;
 +    }
 +
 +    if (!isJS())
 +    {
 +      return new JSONParser().parse(r);
 +    }
 +    // Using a file reader is not currently supported in SwingJS JavaScript
 +
 +    if (r instanceof FileReader)
 +    {
 +      throw new IOException(
 +              "StringJS does not support FileReader parsing for JSON -- but it could...");
 +    }
 +    return JSON.parse(r);
 +
 +  }
 +
 +  /**
 +   * Dump the input stream to an output file.
 +   * 
 +   * @param is
 +   * @param outFile
 +   * @throws IOException
 +   *           if the file cannot be created or there is a problem reading the
 +   *           input stream.
 +   */
 +  public static void streamToFile(InputStream is, File outFile)
 +          throws IOException
 +  {
 +    FileOutputStream fio = new FileOutputStream(outFile);
 +    try
 +    {
 +      if (isJS()
 +              && /**
 +                  * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
 +                  */
 +              true)
 +      {
 +        return;
 +      }
 +      byte[] bb = new byte[32 * 1024];
 +      int l;
 +      while ((l = is.read(bb)) > 0)
 +      {
 +        fio.write(bb, 0, l);
 +      }
 +    } finally
 +    {
 +      fio.close();
 +    }
 +  }
 +
 +  /**
 +   * Add a known domain that implements access-control-allow-origin:*
 +   * 
 +   * These should be reviewed periodically.
 +   * 
 +   * @param domain
 +   *          for a service that is not allowing ajax
 +   * 
 +   * @author hansonr@stolaf.edu
 +   * 
 +   */
 +  public static void addJ2SDirectDatabaseCall(String domain)
 +  {
 +
 +    if (isJS())
 +    {
 +      System.out.println(
 +            "Platform adding known access-control-allow-origin * for domain "
 +                    + domain);
 +      /**
 +       * @j2sNative
 +       * 
 +       *            J2S.addDirectDatabaseCall(domain);
 +       */
 +    }
 +
 +  }
 +
 +  public static void getURLCommandArguments()
 +  {
 +
 +    /**
 +     * Retrieve the first query field as command arguments to Jalview. Include
 +     * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
 +     * element to this value.
 +     * 
 +     * @j2sNative var a =
 +     *            decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
 +     *            + "?").split("?")[1].split("#")[0]); a &&
 +     *            (J2S.thisApplet.__Info.args = a.split(" "));
 +     */
 +
    }
  
+   /**
+    * A (case sensitive) file path comparator that ignores the difference between /
+    * and \
+    * 
+    * @param path1
+    * @param path2
+    * @return
+    */
+   public static boolean pathEquals(String path1, String path2)
+   {
+     if (path1 == null)
+     {
+       return path2 == null;
+     }
+     if (path2 == null)
+     {
+       return false;
+     }
+     String p1 = path1.replace('\\', '/');
+     String p2 = path2.replace('\\', '/');
+     return p1.equals(p2);
+   }
  }
diff --cc src/org/jibble/epsgraphics/EpsGraphics2D.java
index 313ec1c,fe6d962..fe6d962
mode 100644,100755..100644
--- a/src/org/jibble/epsgraphics/EpsGraphics2D.java
+++ b/src/org/jibble/epsgraphics/EpsGraphics2D.java