From 7277d3d8dcfd5f39fe220165e1ea87be62daa25c Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 6 Oct 2014 12:11:11 +0100
Subject: [PATCH] JAL-654_dssp formatting and javadoc

---
 src/MCview/PDBfile.java |   12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 3dd567e..7f5c427 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -241,7 +241,9 @@ public class PDBfile extends jalview.io.AlignFile
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException(MessageManager.getString("exception.outofmemory_loading_pdb_file"));
+      throw new IOException(
+              MessageManager
+                      .getString("exception.outofmemory_loading_pdb_file"));
     } catch (NumberFormatException ex)
     {
       if (line != null)
@@ -305,6 +307,14 @@ public class PDBfile extends jalview.io.AlignFile
     ;
   }
 
+  /**
+   * matches ochains against al and populates seqs with the best match between
+   * each ochain and the set in al
+   * 
+   * @param ochains
+   * @param al
+   * @param dnaOrProtein
+   */
   private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains,
           AlignmentI al, String dnaOrProtein)
   {
-- 
1.7.10.2