From: MorellThomas <morellth@yahoo.co.jp>
Date: Thu, 7 Sep 2023 08:17:49 +0000 (+0200)
Subject: Merge branch 'hardcode'
X-Git-Tag: Release_2_11_4_0~31^2~38
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d17a8d70dedafa76dd0bb6c7c8a280a516464dac;p=jalview.git

Merge branch 'hardcode'
---

d17a8d70dedafa76dd0bb6c7c8a280a516464dac
diff --cc src/jalview/gui/CalculationChooser.java
index af41e58,270383b..816b537
--- a/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
--- a/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);
+   }
  }