X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=e48ff365e90ce54b92919a10fbe00f1c2e033063;hb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;hp=660a4fa05ed1660addab850336c742ba63758177;hpb=2cf0e6316cf8b4e545bad1648966b02fad49017f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 660a4fa..e48ff36 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,6 +1,24 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+
 package jalview.datamodel;
 
-import jalview.jbgui.*;
 import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
@@ -11,6 +29,8 @@ public interface AlignmentI {
   public int         getWidth() ;
   public int         getMaxIdLength() ;
 
+  public boolean isAligned();
+
   public Vector      getSequences();
   public SequenceI   getSequenceAt(int i);
 
@@ -29,7 +49,7 @@ public interface AlignmentI {
   public void        insertColumns(SequenceI[] seqs, int pos) ;
 
   public SequenceI   findName(String name) ;
-  public SequenceI findbyDisplayId(String name);
+  public SequenceI   findbyDisplayId(String name);
 
   public int         findIndex(SequenceI s) ;
 
@@ -48,19 +68,28 @@ public interface AlignmentI {
   public void          addToGroup(SequenceGroup g, SequenceI s) ;
   public void          removeFromGroup(SequenceGroup g,SequenceI s) ;
   public void          addGroup(SequenceGroup sg) ;
-  public SequenceGroup addGroup() ;
   public void          deleteGroup(SequenceGroup g) ;
   public Vector        getGroups();
+  public void deleteAllGroups();
+
+  public void          addSuperGroup(SuperGroup sg);
+  public void          removeSuperGroup(SuperGroup sg);
+  public SuperGroup    getSuperGroup(SequenceGroup sg);
 
   // Sorting
   public void          sortGroups() ;
   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();
 }