JAL-1015 refactor tooltip html generation code to jalview.io.SequenceAnnotationReport

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index c55a519..18b83ae 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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();
 
       PDBChain tmpchain;
-      String line;
+      String line=null;
       boolean modelFlag = false;
       boolean terFlag = false;
       String lastID = "";
 
       int index = 0;
       String atomnam = null;
+      try
+      {
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
@@ -185,6 +185,13 @@ 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);
+      }
+    }
   }
 
   /**