Merge branch 'hardcode'

diff --cc resources/lang/Messages.properties
Simple merge

diff --cc resources/lang/Messages_es.properties
Simple merge

diff --cc src/jalview/analysis/AlignSeq.java
Simple merge

diff --cc src/jalview/gui/CalculationChooser.java
index af41e58,270383b..816b537
--- 1/src/jalview/gui/CalculationChooser.java
--- 2/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@@ -20,6 -20,16 +20,15 @@@
   */
  package jalview.gui;
  
+ import jalview.analysis.TreeBuilder;
+ import jalview.analysis.scoremodels.ScoreModels;
+ import jalview.analysis.scoremodels.SimilarityParams;
+ import jalview.api.analysis.ScoreModelI;
+ import jalview.api.analysis.SimilarityParamsI;
+ import jalview.bin.Cache;
+ import jalview.datamodel.SequenceGroup;
+ import jalview.util.MessageManager;
+ import jalview.viewmodel.AlignmentViewport;
 -
  import java.awt.BorderLayout;
  import java.awt.Color;
  import java.awt.Component;

diff --cc src/jalview/viewmodel/AlignmentViewport.java
index 33cb9dc,8402b32..08444d8
--- 1/src/jalview/viewmodel/AlignmentViewport.java
--- 2/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@@ -20,19 -20,8 +20,20 @@@
   */
  package jalview.viewmodel;
  
 +import java.awt.Color;
 +import java.beans.PropertyChangeSupport;
 +import java.util.ArrayDeque;
 +import java.util.ArrayList;
 +import java.util.BitSet;
 +import java.util.Deque;
 +import java.util.HashMap;
 +import java.util.Hashtable;
 +import java.util.Iterator;
 +import java.util.List;
 +import java.util.Map;
 +
  import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+ import jalview.analysis.Connectivity;
  import jalview.analysis.Conservation;
  import jalview.analysis.TreeModel;
  import jalview.api.AlignCalcManagerI;
@@@ -3122,23 -3098,8 +3123,28 @@@ public abstract class AlignmentViewpor
              false));
    }
  
 +  public void setSavedUpToDate(boolean s)
 +  {
 +    setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);
 +  }
 +
 +  public void setSavedUpToDate(boolean s, QuitHandler.Message m)
 +  {
 +    Console.debug(
 +            "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
 +    savedUpToDate = s;
 +    QuitHandler.setMessage(m);
 +  }
 +
 +  public boolean savedUpToDate()
 +  {
 +    Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
 +            + savedUpToDate);
 +    return savedUpToDate;
 +  }
++
+   public Hashtable<SequenceI, Integer> calculateConnectivity(float[][] scores, byte dim)
+   {
+     return Connectivity.getConnectivity(this, scores, dim);
+   }
  }