From 2ee434fd0b628f004674119095ab3aa893ad6831 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 15 Mar 2013 17:01:49 +0000
Subject: [PATCH] JAL-1140 JAL-674 process with annotate3d and Jmol to get RNA
 and protein secondary structure (will need to refactor this
 when merging to development branch)

---
 src/MCview/PDBfile.java |   24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 95dec13..90328e0 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -24,6 +24,7 @@ import java.awt.*;
 
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
+import jalview.ext.jmol.PDBFileWithJmol;
 import jalview.io.FileParse;
 import jalview.ws.jws1.Annotate3D;
 
@@ -159,7 +160,9 @@ 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 +214,15 @@ 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");
@@ -226,8 +238,10 @@ 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);
+    PDBFileWithJmol jmf = new PDBFileWithJmol(new FileParse(getDataName(),type));
+    Alignment al = new Alignment(jmf.getSeqsAsArray());
+    jmf.addAnnotations(al);
+    replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
   }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");
@@ -286,7 +300,9 @@ 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()));
+          }
         }
       }
     }
-- 
1.7.10.2