Merge branch 'develop' into develop_m2_8_1_2

diff --git a/build.xml b/build.xml
index 47a0188..8e4d44d 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -105,7 +105,7 @@
                <property name="outputJar" value="jalview.jar" />
                <!-- Jalview Applet JMol Jar Dependency -->
                <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
-               <property name="varnaJar" value="VARNAv3-9-dev.jar" />
+               <property name="varnaJar" value="VARNAv3-9.jar" />
                <property name="jalviewLiteJar" value="jalviewApplet.jar" />
                <!-- switch to indicate if we should obfuscate jalviewLite -->
                <!--<property name="donotobfuscate" value="true"/> -->
@@ -157,6 +157,8 @@
                                <include name="plugin.jar"/>
                        </fileset>
                        <pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+
                </path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -457,7 +459,7 @@
                <mkdir dir="${outputDir}" />
                <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
                        classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-                       excludes="ext/**,MCview/**,org/**,vamsas/**" />
+                       excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
        </target>
 
        <target name="packageApplet" depends="compileApplet, buildPropertiesFile">

diff --git a/nbproject/project.properties b/nbproject/project.properties
index 8bee743..b505d62 100644 (file)
--- a/nbproject/project.properties
+++ b/nbproject/project.properties
@@ -71,7 +71,7 @@ file.reference.wsdl4j.jar=lib/wsdl4j.jar
 file.reference.xercesImpl.jar=lib/xercesImpl.jar
 file.reference.xml-apis.jar=lib/xml-apis.jar
 file.reference.miglayout-4.0-swing.jar=lib/miglayout-4.0-swing.jar
-file.reference.varna-3.9-dev.jar=lib/VARNAv3.9-dev.jar
+file.reference.varna-3.9-dev.jar=lib/VARNAv3.9.jar
 includes=**
 jar.compress=false
 javac.classpath=\

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 90328e0..829eed7 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -26,7 +26,6 @@ import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
 import jalview.ext.jmol.PDBFileWithJmol;
 import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -245,10 +244,20 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");
-    Annotate3D an3d = new Annotate3D();
-    // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
-    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
-    replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+    // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+    try {
+    Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+    if (cl!=null)
+    {
+      // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+      Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
+      AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+      replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+    }
+    } catch (ClassNotFoundException x)
+    {
+      //ignore classnotfounds - occurs in applet
+    };
   }
   private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
   {