Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f0d9521..af41e58 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -20,15 +20,6 @@
  */
 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 java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -61,6 +52,15 @@ import javax.swing.JRadioButton;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+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;
+
 /**
  * A dialog where a user can choose and action Tree or PCA calculation options
  */
@@ -130,6 +130,7 @@ public class CalculationChooser extends JPanel
   {
     setLayout(new BorderLayout());
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
     this.setBackground(Color.white);
     frame.addFocusListener(new FocusListener()
@@ -156,12 +157,15 @@ public class CalculationChooser extends JPanel
     pca = new JRadioButton(
             MessageManager.getString("label.principal_component_analysis"));
     pca.setOpaque(false);
+
     neighbourJoining = new JRadioButton(
             MessageManager.getString("label.tree_calc_nj"));
     neighbourJoining.setSelected(true);
+    neighbourJoining.setOpaque(false);
+
     averageDistance = new JRadioButton(
             MessageManager.getString("label.tree_calc_av"));
-    neighbourJoining.setOpaque(false);
+    averageDistance.setOpaque(false);
 
     JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     calcChoicePanel.setOpaque(false);
@@ -271,9 +275,9 @@ public class CalculationChooser extends JPanel
 
     setMinimumSize(new Dimension(325, height - 10));
     String title = MessageManager.getString("label.choose_calculation");
-    if (af.getViewport().viewName != null)
+    if (af.getViewport().getViewName() != null)
     {
-      title = title + " (" + af.getViewport().viewName + ")";
+      title = title + " (" + af.getViewport().getViewName() + ")";
     }
 
     Desktop.addInternalFrame(frame, title, width, height, false);
@@ -291,6 +295,7 @@ public class CalculationChooser extends JPanel
       };
     });
 
+    validateCalcTypes();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
@@ -584,7 +589,13 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
+
+    /*
+     * construct the panel and kick off its calculation thread
+     */
     pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
+    new Thread(pcaPanel).start();
+
   }
 
   /**