X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=931eba62c1cf83b8dda2771187cfe7016a41c665;hb=61aa0f698c7494efa3e6408ce54fac4e8400053c;hp=02397623c0be98194167e36b23d0379e527dd2fe;hpb=521b4513449cabf0e64b9c70c70c304d6bf2f7e3;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 0239762..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
    * 
@@ -480,4 +470,24 @@ public interface AlignViewportI extends ViewStyleI
    *          when true, charWidth/height is set according to font metrics
    */
   void setFont(Font newFont, boolean b);
+
+  /**
+   * Answers true if split screen protein and cDNA use the same font
+   * 
+   * @return
+   */
+  @Override
+  boolean isProteinFontAsCdna();
+
+  /**
+   * Set the flag for whether split screen protein and cDNA use the same font
+   * 
+   * @return
+   */
+  @Override
+  void setProteinFontAsCdna(boolean b);
+
+  public abstract TreeModel getCurrentTree();
+
+  public abstract void setCurrentTree(TreeModel tree);
 }