X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=.classpath;h=c9a8e08bdab1f3358ef0d3313bd9f30958e27463;hb=6c03e40dd457a521bc73c6d5d6bd45688f7db3c7;hp=442795dcd6304344c2054ef5d4c24a39e8bef29f;hpb=64fb69927bb37d8773a75b684a3e7ab3f0c5c212;p=jalview.git

diff --git a/.classpath b/.classpath
index 442795d..c9a8e08 100644
--- a/.classpath
+++ b/.classpath
@@ -1,19 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="src" path="utils"/>
+	<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/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/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
 	<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"/>
@@ -33,39 +33,117 @@
 			<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/Jmol-12.2.4.jar" sourcepath="/Users/jimp/Documents/e6-workspace-new/Jmol/src"/>
-	<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
-	<classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
-	<classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
-	<classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
-	<classpathentry kind="lib" path="lib/groovy-all-1.8.2.jar"/>
-	<classpathentry kind="lib" path="lib/min-jabaws-client-2.1.0.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/VARNAv3-91.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="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.launching.JRE_CONTAINER"/>
 	<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/jersey-json-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/commons-net-3.3.jar" sourcepath="/Users/tcnofoegbu/.m2/repository/commons-net/commons-net/3.3/commons-net-3.3-sources.jar"/>
+	<classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
+	<classpathentry kind="lib" path="j11lib/axis.jar"/>
+	<classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
+	<classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
+	<classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
+	<classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-ant-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-bsf-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-cli-commons-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-cli-picocli-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-console-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-datetime-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-dateutil-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-docgenerator-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-groovydoc-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-groovysh-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-jaxb-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-jmx-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-json-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-json-direct-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-jsr223-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-macro-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-nio-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-servlet-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-sql-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-swing-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-templates-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-test-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-test-junit5-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-testng-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/groovy-xml-2.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
+	<!--  classpathentry kind="lib" path="j11lib/intervalstore-v1.0.jar"/>   -->
+	<classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
+	<classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/java-json.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.activation-api-1.2.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.annotation-api-1.3.2.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.servlet-api-4.0.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
+	<classpathentry kind="lib" path="j11lib/javax.xml.soap-api-1.4.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/jaxb-api-2.3.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jaxb-runtime-2.3.2.jar"/>
+	<classpathentry kind="lib" path="j11lib/jaxws-api-2.3.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
+	<classpathentry kind="lib" path="j11lib/jersey-client-1.19.4.jar"/>
+	<classpathentry kind="lib" path="j11lib/jersey-core-1.19.4.jar"/>
+	<classpathentry kind="lib" path="j11lib/jersey-json-1.19.4.jar"/>
+	<classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j11lib/jetty-io-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j11lib/jetty-server-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j11lib/jetty-util-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/jhall.jar"/>
+	<classpathentry kind="lib" path="j11lib/Jmol-14.29.17-no_netscape.jar"/>
+	<classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j11lib/libquaqua64-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j11lib/log4j-to-slf4j-2.0-rc2.jar"/>
+	<classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
+	<classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
+	<classpathentry kind="lib" path="j11lib/mimepull-1.9.11.jar"/>
+	<classpathentry kind="lib" path="j11lib/policy-2.7.6.jar"/>
+	<classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
+	<classpathentry kind="lib" path="j11lib/regex.jar"/>
+	<classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
+	<classpathentry kind="lib" path="j11lib/slf4j-api-1.7.26.jar"/>
+	<classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.26.jar"/>
+	<classpathentry kind="lib" path="j11lib/stax-ex-1.8.1.jar"/>
+	<classpathentry kind="lib" path="j11lib/stax2-api-4.2.jar"/>
+	<classpathentry kind="lib" path="j11lib/streambuffer-1.5.7.jar"/>
+	<classpathentry kind="lib" path="j11lib/txw2-2.3.2.jar"/>
+	<classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
+	<classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
+	<classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
+	<classpathentry kind="lib" path="j11lib/wsdl4j-1.6.3.jar"/>
+	<classpathentry kind="lib" path="j11lib/xercesImpl.jar"/>
+	<!-- classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/    -->
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
+		<attributes>
+			<attribute name="module" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
+	<classpathentry kind="lib" path="utils/testnglibs/bsh-2.0b4.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/jcommander.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar"/>
+	<classpathentry kind="lib" path="utils/testnglibs/testng.jar"/>
+	<classpathentry kind="lib" path="lib/intervalstore-v1.1.jar"/>
 	<classpathentry kind="output" path="classes"/>
 </classpath>