JAL-674 parser flag to control secondary structure processing

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 7f5c427..bc58c9a 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -42,6 +42,7 @@ public class PDBfile extends jalview.io.AlignFile
   boolean VisibleChainAnnotation = false;
 
   public PDBfile(String inFile, String inType) throws IOException
+  boolean processSecondaryStructure=true;
   {
     super(inFile, inType);
   }
@@ -202,6 +203,8 @@ public class PDBfile extends jalview.io.AlignFile
           }
         }
       }
+      if (processSecondaryStructure)
+      {
       if (rna.size() > 0)
         try
         {
@@ -225,19 +228,7 @@ 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");