Merge branch 'JAL-1422_srs_r281' into develop

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 95dec13..0035914 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -25,7 +25,6 @@ import java.awt.*;
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
 import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -159,7 +158,9 @@ public class PDBfile extends jalview.io.AlignFile
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         entry.setProperty(new Hashtable());
-        entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        if (((PDBChain)chains.elementAt(i)).id!=null) {
+          entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        }
         if (inFile != null)
         {
           entry.setFile(inFile.getAbsolutePath());
@@ -211,6 +212,15 @@ public class PDBfile extends jalview.io.AlignFile
         x.printStackTrace();
         
       };
+      if (prot.size()>0)
+      try {
+        processPdbFileWithJmol(prot);
+      } catch (Exception x)
+      {
+        System.err.println("Exceptions when dealing with RNA in pdb file");
+        x.printStackTrace();
+        
+      };
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -226,15 +236,34 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
   {
-    // process prot sequence with Jmol to get annotated alignment. 
-    // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+    try {
+      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+      if (cl!=null)
+      {
+        Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+        Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+        cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+        replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+      }
+    } catch (ClassNotFoundException q)
+    {}
   }
   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)
   {
@@ -286,7 +315,9 @@ public class PDBfile extends jalview.io.AlignFile
               ap++;
             }
           }
-          annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          if (sq.getAnnotation()!=null) {
+            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          }
         }
       }
     }