X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=b46a1a780c970688dba8fe68407ecf7de479c36f;hb=1a6fbadeec90e7524075ed6e37bbe4b7bba97a94;hp=6a1e026ddacbb933ac3fbd7d3b8bbcc720ea2594;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 6a1e026..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);
 
@@ -29,6 +30,8 @@ public interface AlignmentI {
   public void        insertColumns(SequenceI[] seqs, int pos) ;
 
   public SequenceI   findName(String name) ;
+  public SequenceI   findbyDisplayId(String name);
+
   public int         findIndex(SequenceI s) ;
 
   // Modifying
@@ -42,22 +45,32 @@ public interface AlignmentI {
   // Grouping methods
   public SequenceGroup findGroup(int i) ;
   public SequenceGroup findGroup(SequenceI s) ;
+  public SequenceGroup [] findAllGroups(SequenceI s);
   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() ;
 
-  public void          setGapCharacter(String gc);
-  public String        getGapCharacter();
+  //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();
 }