X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=c18c989dce5b5299d1c0f9d8698695310099ebea;hb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;hp=a6f7d4130527f93aef06a29c32097849d65ce1a2;hpb=2e2e6d269fbaa505151fe777374f41111f2910d5;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a6f7d41..c18c989 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -38,25 +38,10 @@
  */
 package jalview.gui;
 
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
-import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
-import jalview.api.FeatureRenderer;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -79,6 +64,19 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
 
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
 /**
  * DOCUMENT ME!
  * 
@@ -98,12 +96,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   private Rectangle explodedGeometry;
 
-  private FeatureRenderer featureRenderer;
-
-  private boolean includeHiddenRegion = true;
-
-  private AlignExportSettingI exportSettings;
-
   String viewName;
 
   /*
@@ -807,7 +799,7 @@ public class AlignViewport extends AlignmentViewport implements
      * If any cDNA/protein mappings can be made between the alignments, offer to
      * open a linked alignment with split frame option.
      */
-    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
+    if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
     {
       if (AlignmentUtils.isMappable(al, getAlignment()))
       {
@@ -917,6 +909,7 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (openSplitPane)
     {
+      al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment,
               protein.getCodonFrames());
     }
@@ -1035,35 +1028,14 @@ public class AlignViewport extends AlignmentViewport implements
      * is found, the result will be empty.
      */
     SearchResults sr = new SearchResults();
-    int seqOffset = findComplementScrollTarget(sr);
+    int verticalOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
       complementPanel.setFollowingComplementScroll(true);
-      complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.scrollToCentre(sr, verticalOffset);
     }
   }
 
-  @Override
-  public FeatureRenderer getFeatureRenderer()
-  {
-    return featureRenderer;
-  }
-
-  @Override
-  public void setFeatureRenderer(FeatureRenderer featureRenderer)
-  {
-    this.featureRenderer = featureRenderer;
-  }
-
-  public AlignExportSettingI getExportSettings()
-  {
-    return exportSettings;
-  }
-
-  public void setExportSettings(AlignExportSettingI exportSettings)
-  {
-    this.exportSettings = exportSettings;
-  }
 }