From f14d234620501b7b5024a9f98e94c520641e7a09 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:20:57 +0000
Subject: [PATCH] getHiddenSequences

---
 src/jalview/datamodel/Alignment.java  |   10 +++++++++-
 src/jalview/datamodel/AlignmentI.java |    3 ++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b4e2b3f..00d1be8 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,7 +24,6 @@ import jalview.util.*;
 
 import java.util.*;
 
-
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 public class Alignment implements AlignmentI
@@ -41,6 +40,9 @@ public class Alignment implements AlignmentI
     /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
 
+    HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+
     /** Make an alignment from an array of Sequences.
      *
      * @param sequences
@@ -823,4 +825,10 @@ public class Alignment implements AlignmentI
       }
       return modified;
     }
+
+    public HiddenSequences getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 10ea154..7fe4627 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -292,7 +292,8 @@ public interface AlignmentI
      */
     public boolean padGaps();
 
-     public void adjustSequenceAnnotations();
+    public void adjustSequenceAnnotations();
 
+    public HiddenSequences getHiddenSequences();
 
 }
-- 
1.7.10.2