X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2FMCview%2FPDBfile.java;h=3272d1540cf10186704f38b449028100a1ce996a;hb=c07ef0cc5eabc7df4eb15bb3541a702278783f05;hp=829eed7e3a033b7bb39ee04d7bae07c1c23e4023;hpb=8eb35a7bab22595255245c5136dd780816b98f26;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 829eed7..3272d15 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
@@ -24,7 +25,6 @@ import java.awt.*;
 
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
-import jalview.ext.jmol.PDBFileWithJmol;
 import jalview.io.FileParse;
 
 public class PDBfile extends jalview.io.AlignFile
@@ -237,10 +237,17 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
   {
-    PDBFileWithJmol jmf = new PDBFileWithJmol(new FileParse(getDataName(),type));
-    Alignment al = new Alignment(jmf.getSeqsAsArray());
-    jmf.addAnnotations(al);
-    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");