isAligned method added

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 10c8ae1..182b687 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -11,6 +11,8 @@ public interface AlignmentI {
   public int         getWidth() ;\r
   public int         getMaxIdLength() ;\r
 \r
+  public boolean isAligned();\r
+\r
   public Vector      getSequences();\r
   public SequenceI   getSequenceAt(int i);\r
 \r
@@ -29,7 +31,7 @@ public interface AlignmentI {
   public void        insertColumns(SequenceI[] seqs, int pos) ;\r
 \r
   public SequenceI   findName(String name) ;\r
-  public SequenceI findbyDisplayId(String name);\r
+  public SequenceI   findbyDisplayId(String name);\r
 \r
   public int         findIndex(SequenceI s) ;\r
 \r
@@ -44,12 +46,17 @@ public interface AlignmentI {
   // Grouping methods\r
   public SequenceGroup findGroup(int i) ;\r
   public SequenceGroup findGroup(SequenceI s) ;\r
+  public SequenceGroup [] findAllGroups(SequenceI s);\r
   public void          addToGroup(SequenceGroup g, SequenceI s) ;\r
   public void          removeFromGroup(SequenceGroup g,SequenceI s) ;\r
   public void          addGroup(SequenceGroup sg) ;\r
-  public SequenceGroup addGroup() ;\r
   public void          deleteGroup(SequenceGroup g) ;\r
   public Vector        getGroups();\r
+  public void deleteAllGroups();\r
+\r
+  public void          addSuperGroup(SuperGroup sg);\r
+  public void          removeSuperGroup(SuperGroup sg);\r
+  public SuperGroup    getSuperGroup(SequenceGroup sg);\r
 \r
   // Sorting\r
   public void          sortGroups() ;\r