Merge branch 'develop' into menard

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index fe2851a..2005886 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * 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 
@@ -66,19 +66,19 @@ public class PDBfile extends jalview.io.AlignFile
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
-  
-      chains = new Vector();
-
-      PDBChain tmpchain;
-      String line=null;
-      boolean modelFlag = false;
-      boolean terFlag = false;
-      String lastID = "";
-
-      int index = 0;
-      String atomnam = null;
-      try
-      {
+
+    chains = new Vector();
+
+    PDBChain tmpchain;
+    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)
@@ -221,10 +221,10 @@ 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)
+    } catch (NumberFormatException ex)
     {
-      if (line!=null) {
+      if (line != null)
+      {
         System.err.println("Couldn't read number from line:");
         System.err.println(line);
       }