xrefs retrieved from Uniprot

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c9a383f..2ad32f0 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -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()