X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=931eba62c1cf83b8dda2771187cfe7016a41c665;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=9e6d1c05b955f2d895be047a313e755168f23121;hpb=8181358395df043e2554381f84229cc0e0323011;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9e6d1c0..931eba6 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,10 +21,10 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -243,16 +243,6 @@ public interface AlignViewportI extends ViewStyleI
   void clearSequenceColours();
 
   /**
-   * This method returns the visible alignment as text, as seen on the GUI, ie
-   * if columns are hidden they will not be returned in the result. Use this for
-   * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
-   * @return String[]
-   */
-  CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
-  /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
    * 
@@ -486,6 +476,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   boolean isProteinFontAsCdna();
 
   /**
@@ -493,5 +484,10 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   void setProteinFontAsCdna(boolean b);
+
+  public abstract TreeModel getCurrentTree();
+
+  public abstract void setCurrentTree(TreeModel tree);
 }