X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=d221d37d1b1050c5842272cd0718000efa773921;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=b66fb111c19b19e079039a6ecb2ea7b4c056bca1;hpb=9282440c3bafe52674446b861a6b43d9bcfa3664;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index b66fb11..d221d37 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -20,7 +20,6 @@
  */
 package jalview.io;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
@@ -48,7 +47,8 @@ public abstract class AlignFile extends FileParse
   int maxLength = 0;
 
   /**
-   * Sequences to be added to form a new alignment.
+   * Sequences to be added to form a new alignment. TODO: remove vector in this
+   * class
    */
   protected Vector<SequenceI> seqs;
 
@@ -200,7 +200,7 @@ public abstract class AlignFile extends FileParse
    * 
    * @param al
    */
-  public void addAnnotations(Alignment al)
+  public void addAnnotations(AlignmentI al)
   {
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
@@ -220,6 +220,11 @@ public abstract class AlignFile extends FileParse
 
   }
 
+  /**
+   * register sequence groups on the alignment for **output**
+   * 
+   * @param al
+   */
   public void addSeqGroups(AlignmentI al)
   {
     this.seqGroups = al.getGroups();
@@ -233,7 +238,7 @@ public abstract class AlignFile extends FileParse
    * @note implicitly called by addAnnotations()
    * @param al
    */
-  public void addProperties(Alignment al)
+  public void addProperties(AlignmentI al)
   {
     if (properties != null && properties.size() > 0)
     {
@@ -378,4 +383,13 @@ public abstract class AlignFile extends FileParse
     return newickStrings == null ? 0 : newickStrings.size();
   }
 
+  public void addGroups(AlignmentI al)
+  {
+
+    for (SequenceGroup sg : getSeqGroups())
+    {
+      al.addGroup(sg);
+    }
+  }
+
 }