X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=a6ad951cb0b2658dab9aef8ec86c65f17dee3cbe;hb=aa030270d61a25a3417f674c48c2d323ff238277;hp=255eee043b32ad338532c0ec91ad29cec5255197;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 255eee0..a6ad951 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * 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.
- * 
+ *  
  * 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 
@@ -56,18 +56,18 @@ public class PDBfile extends jalview.io.AlignFile
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
 
-    try
-    {
-      chains = new Vector();
+    chains = new Vector();
 
-      PDBChain tmpchain;
-      String line;
-      boolean modelFlag = false;
-      boolean terFlag = false;
-      String lastID = "";
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
 
-      int index = 0;
-      String atomnam = null;
+    int index = 0;
+    String atomnam = null;
+    try
+    {
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
@@ -184,6 +184,13 @@ public class PDBfile extends jalview.io.AlignFile
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
       throw new IOException("Out of memory loading PDB File");
+    } catch (NumberFormatException ex)
+    {
+      if (line != null)
+      {
+        System.err.println("Couldn't read number from line:");
+        System.err.println(line);
+      }
     }
   }