use OOMwarning to warn user when out of Memory occurs

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c9a383f..c38fad3 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -71,7 +71,17 @@ public abstract class AlignFile
 
     parse();
   }
-
+  /**
+   * Attempt to read from the position where some other parsing process left off.
+   * @param source
+   * @throws IOException
+   */
+  public AlignFile(FileParse source) throws IOException
+  {
+    super(source);
+    initData();
+    parse();
+  }
   /**
    * Return the seqs Vector
    */
@@ -234,17 +244,17 @@ public abstract class AlignFile
     return seq.getDisplayId(jvSuffix);
   }
   /**
-   * vector of String[] treeName, newickString pairs 
+   * vector of String[] treeName, newickString pairs
    */
   Vector newickStrings=null;
-  
+
   protected void addNewickTree(String treeName, String newickString)
   {
     if (newickStrings == null)
     {
       newickStrings = new Vector();
     }
-    newickStrings.add(new String[] { treeName, newickString});
+    newickStrings.addElement(new String[] { treeName, newickString});
   }
 
   protected int getTreeCount()