added preferences for usage stats, questionnaire check and version check.

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 5fd3d10..b368b91 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -55,7 +55,7 @@ public class PDBfile extends jalview.io.AlignFile
   public void parse() throws IOException
   {
     // TODO set the filename sensibly
-    id = (inFile == null) ? "PDBFILE" : inFile.getName();
+    id = (inFile == null || inFile.getName()==null || inFile.getName().length()==0) ? "PDBFILE" : inFile.getName();
     try
     {
       chains = new Vector();
@@ -70,8 +70,20 @@ public class PDBfile extends jalview.io.AlignFile
       {
         if (line.indexOf("HEADER") == 0)
         {
-          id = line.substring(62, 67).trim();
-          continue;
+          if (line.length()>62)
+          {
+            String tid;
+            if (line.length()>67) {
+              tid = line.substring(62, 67).trim();
+            } else {
+              tid=line.substring(62).trim();
+            }
+            if (tid.length()>0)
+            {
+              id = tid;
+            }
+            continue;
+          }
         }
         // Were we to do anything with SEQRES - we start it here
         if (line.indexOf("SEQRES") == 0)