X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=7b1e84ad13580a1efd2244a16de90d92474377f6;hb=0669bcd76c254141146c1fc2628812c782571c0b;hp=a603ccac45d6d9577a076be41a481c2bf253230c;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index a603cca..7b1e84a 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -72,8 +72,21 @@ public abstract class AlignFile extends FileParse
 
   long end;
 
+  /**
+   * true if parse() has been called
+   */
   private boolean parseCalled;
 
+  private boolean parseImmediately;
+
+  /**
+   * @return if doParse() was called at construction time
+   */
+  protected boolean isParseImmediately()
+  {
+    return parseImmediately;
+  }
+
   /**
    * Creates a new AlignFile object.
    */
@@ -153,6 +166,11 @@ public abstract class AlignFile extends FileParse
   {
     super(source);
     initData();
+
+    // stash flag in case parse needs to know if it has to autoconfigure or was
+    // configured after construction
+    this.parseImmediately = parseImmediately;
+
     if (parseImmediately)
     {
       doParse();
@@ -174,11 +192,6 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
-    // sets the index of each sequence in the alignment
-    for (int i = 0, c = seqs.size(); i < c; i++)
-    {
-      seqs.get(i).setIndex(i);
-    }
   }
 
   /**