From eb735a1925bb9387a532f3f89b6eba3eab695e85 Mon Sep 17 00:00:00 2001
From: tva <tva@10.205.251.175>
Date: Wed, 5 Jun 2019 13:24:28 +0100
Subject: [PATCH] JAL-3285 add unmerged features to AlignViewport

---
 src/jalview/gui/AlignViewport.java |   50 +++++++++++++++++++++---------------
 1 file changed, 29 insertions(+), 21 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 847084d..0b40abd 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -92,12 +92,6 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  boolean validCharWidth;
-
-  public boolean followSelection = true;
-
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
   /**
    * Creates a new AlignViewport object.
    * 
@@ -260,18 +254,13 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    AlignmentI al = getAlignment();
-
-    if (Cache.getDefault("NORMALISE_GAPS", true))
-    {
-      al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-    }
+		alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
-    if (consensusProfiles == null && !isDataset)
+		if (hconsensus == null && !isDataset)
     {
-      if (!al.isNucleotide())
+			if (!alignment.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -295,7 +284,7 @@ public class AlignViewport extends AlignmentViewport
     initAutoAnnotation();
     // initInformation();
 
-    String colourProperty = al.isNucleotide()
+		String colourProperty = alignment.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -318,10 +307,12 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(consensusProfiles);
+			residueShading.setConsensus(hconsensus);
     }
     setColourAppliesToAllGroups(true);
   }
+  
+  boolean validCharWidth;
 
   /**
    * {@inheritDoc}
@@ -405,9 +396,9 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (getAlignment() != null && align != null)
+		if (alignment != null && align != null)
     {
-      getAlignment().setCodonFrames(align.getCodonFrames());
+      alignment.setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -476,11 +467,11 @@ public class AlignViewport extends AlignmentViewport
     }
     else
     {
-      end = getAlignment().getWidth();
+      end = alignment.getWidth();
     }
 
-    return getAlignment().getHiddenColumns().getVisContigsIterator(start,
-            end, false);
+    return (alignment.getHiddenColumns().getVisContigsIterator(start,
+            end, false));
   }
 
   /**
@@ -529,6 +520,8 @@ public class AlignViewport extends AlignmentViewport
     return false;
   }
 
+  public boolean followSelection = true;
+  
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -593,6 +586,19 @@ public class AlignViewport extends AlignmentViewport
     return StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
   }
+  
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  @Override
+public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
 
   /**
    * 
@@ -603,6 +609,8 @@ public class AlignViewport extends AlignmentViewport
   {
     return validCharWidth;
   }
+  
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
-- 
1.7.10.2