From 6a8d4183e249a9db0f46a1da7ab795c4454d219a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 2 Aug 2007 10:16:46 +0000
Subject: [PATCH] javadoc and bugfix for 'save' when jalview is default format

---
 src/jalview/gui/AlignFrame.java |   15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6302efb..f678915 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -59,9 +59,13 @@ public class AlignFrame
   Vector alignPanels = new Vector();
 
 
-  /** DOCUMENT ME!! */
+  /** 
+   * Last format used to load or save alignments in this window 
+   */
   String currentFileFormat = null;
-
+  /**
+   * Current filename for this alignment
+   */
   String fileName = null;
 
 
@@ -725,8 +729,11 @@ public class AlignFrame
                                     currentFileFormat);
 
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-
-      saveAlignment(fileName, currentFileFormat.substring(0,currentFileFormat.indexOf(" ")));
+      if (currentFileFormat.indexOf(" ")>-1)
+      {
+        currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" "));
+      }
+      saveAlignment(fileName, currentFileFormat);
     }
   }
 
-- 
1.7.10.2