X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=b976a3d94d1f51c9f9488d171821ebe217913ff4;hb=fc895e8dacdbb7f49df0ec5c9f475b841082e9b3;hp=248bae2bba09a6de500722b2847a74940e82d26b;hpb=173f77ac7161e8866ddfe6b5689d61a83f459cfc;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 248bae2..b976a3d 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -23,9 +23,9 @@ package jalview.api;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -244,16 +244,6 @@ 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
    * 
@@ -487,6 +477,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   boolean isProteinFontAsCdna();
 
   /**
@@ -494,9 +485,19 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   void setProteinFontAsCdna(boolean b);
 
-  public abstract TreeModel getCurrentTree();
+  TreeModel getCurrentTree();
 
-  public abstract void setCurrentTree(TreeModel tree);
+  void setCurrentTree(TreeModel tree);
+
+  /**
+   * Answers a data bean containing data for export as configured by the
+   * supplied options
+   * 
+   * @param options
+   * @return
+   */
+  AlignmentExportData getAlignExportData(AlignExportSettingsI options);
 }