From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 31 May 2016 16:52:29 +0000 (+0100)
Subject: JAL-1944 fix for visible seqs sometimes been replaced with hidden ones while exportin... 
X-Git-Tag: Release_2_10_0~198
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3f06233fb50a383439b4e0f28405b8681c2e2d72;p=jalview.git

JAL-1944 fix for visible seqs sometimes been replaced with hidden ones while exporting sequences with the option 'Export Hidden Sequences' set to false
---

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 45e77ba..f40b73b 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -376,5 +376,20 @@ 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 d9d5f27..895f2f6 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1313,6 +1313,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {
+      viewport.setExportHiddenSeqs(settings.isExportHiddenSequences());
       omitHidden = viewport.getViewAsString(false);
     }
 
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c16fdce..6581bef 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1601,7 +1601,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows())
+      if (hasHiddenRows() && isExportHiddenSeqs)
       {
         iSize = alignment.getHiddenSequences().getFullAlignment()
                 .getHeight();
@@ -2719,4 +2719,18 @@ 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;
+  }
 }