Cleanup, note: rectangular selection works by holding mouse wheel and s (see line...

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 9e596e2..21d985c 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -28,7 +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;
 import java.awt.Component;
@@ -61,6 +61,15 @@ 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
  */
@@ -80,13 +89,13 @@ public class CalculationChooser extends JPanel
 
   private static final int MIN_PCA_SELECTION = 4;
 
-  private static final int MIN_PASIMAP_SELECTION = 4; //&! <++>!! chekc how many
+  private static final int MIN_PASIMAP_SELECTION = 8; 
 
   AlignFrame af;
 
   JRadioButton pca;
 
-  JRadioButton pasimap;        //&! initialize JRadioButton object for pasimap
+  JRadioButton pasimap;        
 
   JRadioButton neighbourJoining;
 
@@ -115,7 +124,6 @@ public class CalculationChooser extends JPanel
    */
   private PCAPanel pcaPanel;
 
-  //&! 
   private PaSiMapPanel pasimapPanel;
 
   /**
@@ -137,6 +145,7 @@ 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()
@@ -197,7 +206,7 @@ public class CalculationChooser extends JPanel
     pcaBorderless.add(pca, FlowLayout.LEFT);
     calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
 
-    //&! create pasimap panel
+    // create pasimap panel
     JPanel pasimapBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));    // create new JPanel (button) for pasimap
     pasimapBorderless.setBorder(
            BorderFactory.createEmptyBorder(2, b.left, 2, b.right));    // set border (margin) for button (same as treePanel and pca)
@@ -212,7 +221,7 @@ public class CalculationChooser extends JPanel
 
     ButtonGroup calcTypes = new ButtonGroup();
     calcTypes.add(pca);
-    calcTypes.add(pasimap);    //&! add pasimap to the calculation types
+    calcTypes.add(pasimap);
     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);
 
@@ -656,7 +665,6 @@ public class CalculationChooser extends JPanel
     /*
      * construct the panel and kick off its calculation thread
      */
-    //&! change to PaSiMapPanel
     pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName, params);
     new Thread(pasimapPanel).start();