From 142304c420500eb47ea9af5b9be156caf4afaafd Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 11 Oct 2017 08:20:21 +0100
Subject: [PATCH] JAL-2742 removed unused getViewAsCigars

---
 src/jalview/api/AlignViewportI.java          |   13 ++-----------
 src/jalview/viewmodel/AlignmentViewport.java |    8 --------
 2 files changed, 2 insertions(+), 19 deletions(-)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9e6d1c0..3cb06c1 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -24,7 +24,6 @@ import jalview.analysis.Conservation;
 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 +242,6 @@ 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 +475,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   boolean isProteinFontAsCdna();
 
   /**
@@ -493,5 +483,6 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   void setProteinFontAsCdna(boolean b);
 }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3702cd0..b260cab 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -33,7 +33,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
@@ -1673,13 +1672,6 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    return new CigarArray(alignment, alignment.getHiddenColumns(),
-            (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
-- 
1.7.10.2