Fix alignment and score calculation for cc_analysis

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 0f6c257..270383b 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -28,6 +28,7 @@ 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;
@@ -115,8 +116,8 @@ public class CalculationChooser extends JPanel
    */
   private PCAPanel pcaPanel;
 
-  //&! change to PaSiMapPanel
-  private PCAPanel pasimapPanel;
+  //&! 
+  private PaSiMapPanel pasimapPanel;
 
   /**
    * Constructor
@@ -656,8 +657,7 @@ public class CalculationChooser extends JPanel
     /*
      * construct the panel and kick off its calculation thread
      */
-    //&! change to PaSiMapPanel
-    pasimapPanel = new PCAPanel(af.alignPanel, modelName, params);
+    pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName, params);
     new Thread(pasimapPanel).start();
 
   }