X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=4d9d7381175c9ca1851506f9fbf7e14d2ea15b68;hb=60403f610c291791bf7c58f9c7232206469687cd;hp=8a826a1521c020b8190f268a6832efd310e8eedd;hpb=aa3069cd07bbd5b35b10d5893fa90a59382e5f82;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 8a826a1..4d9d738 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -22,19 +22,9 @@ import java.util.*;
 
 import java.awt.*;
 
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
 import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -47,12 +37,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(String inFile, String inType) throws IOException
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -62,7 +52,7 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public void parse() throws IOException
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
@@ -235,16 +225,25 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
   {
-//    System.out.println("this is a PDB format and RNA sequence");
-    Annotate3D an3d = new Annotate3D();
-    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
-    replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+    // process prot sequence with Jmol to get annotated alignment. 
+    // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
   }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");
-    Annotate3D an3d = new Annotate3D();
-    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)
   {