Merge branch 'develop' into features/mchmmer

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 96fea6e..862c4fb 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -35,7 +35,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
@@ -57,11 +56,9 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
-import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JInternalFrame;
 
@@ -282,6 +279,10 @@ public class AlignViewport extends AlignmentViewport
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
+      // for now, use consensus options for Information till it gets its own
+      setShowHMMSequenceLogo(showSequenceLogo);
+      setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+      setShowInformationHistogram(showConsensusHistogram);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
 
@@ -588,23 +589,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
-  @Override
-  public boolean isNormaliseSequenceLogo()
-  {
-    return normaliseSequenceLogo;
-  }
-
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
-  public void setNormaliseHMMSequenceLogo(boolean state)
-  {
-    normaliseHMMSequenceLogo = state;
-  }
-
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -1045,10 +1029,4 @@ public class AlignViewport extends AlignmentViewport
     fr.setTransparency(featureSettings.getTransparency());
   }
 
-  @Override
-  public boolean isNormaliseHMMSequenceLogo()
-  {
-    return normaliseHMMSequenceLogo;
-  }
-
 }