Merge branch 'develop' into develop_m2_8_1_2

[jalview.git] / src / MCview / PDBfile.java

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)
   {