getHiddenSequences

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 10ea154..7fe4627 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -292,7 +292,8 @@ public interface AlignmentI
      */\r
     public boolean padGaps();\r
 \r
-     public void adjustSequenceAnnotations();\r
+    public void adjustSequenceAnnotations();\r
 \r
+    public HiddenSequences getHiddenSequences();\r
 \r
 }\r