From e7b6c76c3b028aeeef7770c99c87d895c1b46172 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 1 Jun 2016 16:33:46 +0100
Subject: [PATCH] JAL-1944 updated bugfix implementation

---
 src/jalview/api/AlignViewportI.java          |   27 +++++++++++++-------------
 src/jalview/gui/AlignFrame.java              |    4 ++--
 src/jalview/viewmodel/AlignmentViewport.java |   19 +++++++-----------
 3 files changed, 22 insertions(+), 28 deletions(-)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f40b73b..9d5c075 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -240,6 +240,19 @@ public interface AlignViewportI extends ViewStyleI
    * @return String[]
    */
   String[] getViewAsString(boolean selectedRegionOnly);
+  
+  /**
+   * 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. However, If
+   * there are hidden sequences, isExportHiddenSeqs flag decides if they would
+   * be exported or not. Use this for calculating trees, PCA, redundancy etc on
+   * views which contain hidden columns.
+   * 
+   * @param selectedRegionOnly
+   * @param isExportHiddenSeqs
+   * @return String[]
+   */
+  String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -376,20 +389,6 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-  /**
-   * Set whether hidden Sequences should be trimmed off during an export
-   * operation.
-   * 
-   * @param isExportHiddenSeqs
-   */
-  public void setExportHiddenSeqs(boolean isExportHiddenSeqs);
-
-  /**
-   * If true hidden Sequences are exported otherwise they aren't
-   * 
-   * @return
-   */
-  public boolean isExportHiddenSeqs();
 
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 818c150..d973bb7 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1313,8 +1313,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {
-      viewport.setExportHiddenSeqs(settings.isExportHiddenSequences());
-      omitHidden = viewport.getViewAsString(false);
+      omitHidden = viewport.getViewAsString(false,
+              settings.isExportHiddenSequences());
     }
 
     int[] alignmentStartEnd = new int[2];
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 6581bef..7cea5a3 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1588,6 +1588,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
+    return getViewAsString(selectedRegionOnly, true);
+  }
+
+  @Override
+  public String[] getViewAsString(boolean selectedRegionOnly,
+          boolean isExportHiddenSeqs)
+  {
     String[] selection = null;
     SequenceI[] seqs = null;
     int i, iSize;
@@ -2720,17 +2727,5 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
-  private boolean isExportHiddenSeqs = true;
 
-  @Override
-  public void setExportHiddenSeqs(boolean isExportHiddenSeqs)
-  {
-    this.isExportHiddenSeqs = isExportHiddenSeqs;
-  }
-
-  @Override
-  public boolean isExportHiddenSeqs()
-  {
-    return isExportHiddenSeqs;
-  }
 }
-- 
1.7.10.2