X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=b46a1a780c970688dba8fe68407ecf7de479c36f;hb=4c61bddcb9e367db694e3f2bde9c4d25f114f50b;hp=80b22ae2af1f9eea80b9e1a426ad8c660e0a2ddd;hpb=3ac9a19998fe3b2f4e4583bed327a13ca80c874b;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 80b22ae..b46a1a7 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,6 +1,5 @@
 package jalview.datamodel;
 
-import jalview.jbgui.*;
 import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
@@ -11,6 +10,8 @@ public interface AlignmentI {
   public int         getWidth() ;
   public int         getMaxIdLength() ;
 
+  public boolean isAligned();
+
   public Vector      getSequences();
   public SequenceI   getSequenceAt(int i);
 
@@ -61,10 +62,15 @@ public interface AlignmentI {
   public void          sortByPID(SequenceI s) ;
   public void          sortByID() ;
 
+  //Annotations
+  public void addAnnotation(AlignmentAnnotation aa);
+  public void deleteAnnotation(AlignmentAnnotation aa);
+  public AlignmentAnnotation [] getAlignmentAnnotation();
+
   public void          setGapCharacter(char gc);
   public char          getGapCharacter();
 
-    public Vector        getAAFrequency();
+  public Vector        getAAFrequency();
 }