JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4d9d738..4fc8814 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * 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;
 
@@ -158,7 +161,9 @@ 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());
@@ -210,6 +215,15 @@ 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");
@@ -225,8 +239,17 @@ 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");
@@ -295,7 +318,9 @@ 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()));
+          }
         }
       }
     }