Merge branch 'releases/Release_2_11_4_Branch'

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 183419e..8e5cc9e 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -25,9 +25,11 @@ import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 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.datamodel.SequenceGroup;
 import jalview.util.MessageManager;

-
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;

 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;

@@ -60,6 +62,18 @@ import javax.swing.JRadioButton;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 

+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.ScoreMatrix;
+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.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+

 /**
  * A dialog where a user can choose and action Tree or PCA calculation options
  */
 /**
  * A dialog where a user can choose and action Tree or PCA calculation options
  */

@@ -75,20 +89,50 @@ public class CalculationChooser extends JPanel
 
   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
 
 
   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
 

+  private static final int MIN_PAIRWISE_SELECTION = 2;
+

   private static final int MIN_TREE_SELECTION = 3;
 
   private static final int MIN_PCA_SELECTION = 4;
 
   private static final int MIN_TREE_SELECTION = 3;
 
   private static final int MIN_PCA_SELECTION = 4;
 

+  private String secondaryStructureModelName;
+
+  private void getSecondaryStructureModelName()
+  {
+
+    ScoreModels scoreModels = ScoreModels.getInstance();
+    for (ScoreModelI sm : scoreModels.getModels())
+    {
+      if (sm.isSecondaryStructure())
+      {
+        secondaryStructureModelName = sm.getName();
+      }
+    }
+
+  }
+
+  /**
+   * minimum number of sequences needed for PASIMAP is 9 (so each has 8
+   * connections)
+   */
+  private static final int MIN_PASIMAP_SELECTION = 9;
+

   AlignFrame af;
 
   AlignFrame af;
 

+  JRadioButton pairwise;
+

   JRadioButton pca;
 
   JRadioButton pca;
 

+  JRadioButton pasimap;
+

   JRadioButton neighbourJoining;
 
   JRadioButton averageDistance;
 
   JComboBox<String> modelNames;
 
   JRadioButton neighbourJoining;
 
   JRadioButton averageDistance;
 
   JComboBox<String> modelNames;
 

+  JComboBox<String> ssSourceDropdown;
+

   JButton calculate;
 
   private JInternalFrame frame;
   JButton calculate;
 
   private JInternalFrame frame;

@@ -103,13 +147,15 @@ public class CalculationChooser extends JPanel
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 

-  List<String> tips = new ArrayList<String>();
+  List<String> tips = new ArrayList<>();

 
   /*
    * the most recently opened PCA results panel
    */
   private PCAPanel pcaPanel;
 
 
   /*
    * the most recently opened PCA results panel
    */
   private PCAPanel pcaPanel;
 

+  private PaSiMapPanel pasimapPanel;
+

   /**
    * Constructor
    * 
   /**
    * Constructor
    * 

@@ -120,6 +166,7 @@ public class CalculationChooser extends JPanel
     this.af = alignFrame;
     init();
     af.alignPanel.setCalculationDialog(this);
     this.af = alignFrame;
     init();
     af.alignPanel.setCalculationDialog(this);

+

   }
 
   /**
   }
 
   /**

@@ -127,8 +174,10 @@ public class CalculationChooser extends JPanel
    */
   void init()
   {
    */
   void init()
   {

+    getSecondaryStructureModelName();

     setLayout(new BorderLayout());
     frame = new JInternalFrame();
     setLayout(new BorderLayout());
     frame = new JInternalFrame();

+    frame.setFrameIcon(null);

     frame.setContentPane(this);
     this.setBackground(Color.white);
     frame.addFocusListener(new FocusListener()
     frame.setContentPane(this);
     this.setBackground(Color.white);
     frame.addFocusListener(new FocusListener()

@@ -155,12 +204,24 @@ public class CalculationChooser extends JPanel
     pca = new JRadioButton(
             MessageManager.getString("label.principal_component_analysis"));
     pca.setOpaque(false);
     pca = new JRadioButton(
             MessageManager.getString("label.principal_component_analysis"));
     pca.setOpaque(false);

+
+    pasimap = new JRadioButton( // create the JRadioButton for pasimap with
+                                // label.pasimap as its text
+            MessageManager.getString("label.pasimap"));
+    pasimap.setOpaque(false);
+

     neighbourJoining = new JRadioButton(
             MessageManager.getString("label.tree_calc_nj"));
     neighbourJoining.setSelected(true);
     neighbourJoining = new JRadioButton(
             MessageManager.getString("label.tree_calc_nj"));
     neighbourJoining.setSelected(true);

+    neighbourJoining.setOpaque(false);
+

     averageDistance = new JRadioButton(
             MessageManager.getString("label.tree_calc_av"));
     averageDistance = new JRadioButton(
             MessageManager.getString("label.tree_calc_av"));

-    neighbourJoining.setOpaque(false);
+    averageDistance.setOpaque(false);
+
+    pairwise = new JRadioButton(
+            MessageManager.getString("action.pairwise_alignment"));
+    pairwise.setOpaque(false);

 
     JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     calcChoicePanel.setOpaque(false);
 
     JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     calcChoicePanel.setOpaque(false);

@@ -182,15 +243,53 @@ public class CalculationChooser extends JPanel
     pcaBorderless.add(pca, FlowLayout.LEFT);
     calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
 
     pcaBorderless.add(pca, FlowLayout.LEFT);
     calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
 

+    // 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)
+    pasimapBorderless.setOpaque(false); // false -> stops every pixel inside
+                                        // border from being painted
+    pasimapBorderless.add(pasimap, FlowLayout.LEFT); // add pasimap button to
+    // the JPanel
+    if (!Platform.isJS())
+    {
+      // FIXME JAL-4443
+      calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button
+                                                               // with
+      // border and
+      // everything to
+      // the overall
+      // ChoicePanel
+    }
+

     treePanel.add(neighbourJoining);
     treePanel.add(averageDistance);
 
     calcChoicePanel.add(treePanel);
     treePanel.add(neighbourJoining);
     treePanel.add(averageDistance);
 
     calcChoicePanel.add(treePanel);

+    calcChoicePanel.add(pairwise, FlowLayout.CENTER);

 
     ButtonGroup calcTypes = new ButtonGroup();
     calcTypes.add(pca);
 
     ButtonGroup calcTypes = new ButtonGroup();
     calcTypes.add(pca);

+    if (!Platform.isJS())
+    {
+      // FIXME JAL-4443
+      calcTypes.add(pasimap);
+    }

     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);
     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);

+    calcTypes.add(pairwise);

 
     ActionListener calcChanged = new ActionListener()
     {
 
     ActionListener calcChanged = new ActionListener()
     {

@@ -201,17 +300,44 @@ public class CalculationChooser extends JPanel
       }
     };
     pca.addActionListener(calcChanged);
       }
     };
     pca.addActionListener(calcChanged);

+    pasimap.addActionListener(calcChanged); // add the calcChanged
+                                            // ActionListener to pasimap -->
+                                            // <++> idk

     neighbourJoining.addActionListener(calcChanged);
     averageDistance.addActionListener(calcChanged);
 
     neighbourJoining.addActionListener(calcChanged);
     averageDistance.addActionListener(calcChanged);
 

+    // to do
+    ssSourceDropdown = buildSSSourcesOptionsList();
+    ssSourceDropdown.setVisible(false); // Initially hide the dropdown
+    pairwise.addActionListener(calcChanged);

     /*
      * score models drop-down - with added tooltips!
      */
     modelNames = buildModelOptionsList();
 
     /*
      * score models drop-down - with added tooltips!
      */
     modelNames = buildModelOptionsList();
 

+    // Step 3: Show or Hide Dropdown Based on Selection
+    modelNames.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        String selectedModel = modelNames.getSelectedItem().toString();
+
+        if (selectedModel.equals(secondaryStructureModelName))
+        {
+          ssSourceDropdown.setVisible(true);
+        }
+        else
+        {
+          ssSourceDropdown.setVisible(false);
+        }
+      }
+    });
+

     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
     scoreModelPanel.setOpaque(false);
     scoreModelPanel.add(modelNames);
     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
     scoreModelPanel.setOpaque(false);
     scoreModelPanel.add(modelNames);

+    scoreModelPanel.add(ssSourceDropdown);

 
     /*
      * score model parameters
 
     /*
      * score model parameters

@@ -265,7 +391,7 @@ public class CalculationChooser extends JPanel
     }
     this.add(actionPanel, BorderLayout.SOUTH);
 
     }
     this.add(actionPanel, BorderLayout.SOUTH);
 

-    int width = 350;
+    int width = 365;

     int height = includeParams ? 420 : 240;
 
     setMinimumSize(new Dimension(325, height - 10));
     int height = includeParams ? 420 : 240;
 
     setMinimumSize(new Dimension(325, height - 10));

@@ -290,6 +416,7 @@ public class CalculationChooser extends JPanel
       };
     });
 
       };
     });
 

+    validateCalcTypes();

     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 

@@ -309,12 +436,18 @@ public class CalculationChooser extends JPanel
      * return value of true means enabled and selected
      */
     boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION);
      * return value of true means enabled and selected
      */
     boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION);

+    boolean checkPasimap = checkEnabled(pasimap, size,
+            MIN_PASIMAP_SELECTION); // check if pasimap is enabled and min_size
+                                    // is fulfilled

     boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size,
             MIN_TREE_SELECTION);
     boolean checkAverageDistance = checkEnabled(averageDistance, size,
             MIN_TREE_SELECTION);
     boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size,
             MIN_TREE_SELECTION);
     boolean checkAverageDistance = checkEnabled(averageDistance, size,
             MIN_TREE_SELECTION);

+    boolean checkPairwise = checkEnabled(pairwise, size,
+            MIN_PAIRWISE_SELECTION);

 
 

-    if (checkPca || checkNeighbourJoining || checkAverageDistance)
+    if (checkPca || checkPasimap || checkPca || checkNeighbourJoining
+            || checkAverageDistance || checkPairwise)

     {
       calculate.setToolTipText(null);
       calculate.setEnabled(true);
     {
       calculate.setToolTipText(null);
       calculate.setEnabled(true);

@@ -375,7 +508,7 @@ public class CalculationChooser extends JPanel
    */
   protected JComboBox<String> buildModelOptionsList()
   {
    */
   protected JComboBox<String> buildModelOptionsList()
   {

-    final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+    final JComboBox<String> scoreModelsCombo = new JComboBox<>();

     scoreModelsCombo.setRenderer(renderer);
 
     /*
     scoreModelsCombo.setRenderer(renderer);
 
     /*

@@ -413,50 +546,152 @@ public class CalculationChooser extends JPanel
     return scoreModelsCombo;
   }
 
     return scoreModelsCombo;
   }
 

+  private JComboBox<String> buildSSSourcesOptionsList()
+  {
+    final JComboBox<String> comboBox = new JComboBox<>();
+    Object curSel = comboBox.getSelectedItem();
+    DefaultComboBoxModel<String> sourcesModel = new DefaultComboBoxModel<>();
+
+    List<String> ssSources = getApplicableSecondaryStructureSources();
+
+    boolean selectedIsPresent = false;
+    for (String source : ssSources)
+    {
+      if (curSel != null && source.equals(curSel))
+      {
+        selectedIsPresent = true;
+        curSel = source;
+      }
+      sourcesModel.addElement(source);
+
+    }
+
+    if (selectedIsPresent)
+    {
+      sourcesModel.setSelectedItem(curSel);
+    }
+    comboBox.setModel(sourcesModel);
+
+    return comboBox;
+  }
+

   private void updateScoreModels(JComboBox<String> comboBox,
           List<String> toolTips)
   {
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
   private void updateScoreModels(JComboBox<String> comboBox,
           List<String> toolTips)
   {
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();

-    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+
+    /*
+     * select the score models applicable to the alignment type
+     */
+    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+    AlignmentAnnotation[] alignmentAnnotations = af.getViewport()
+            .getAlignment().getAlignmentAnnotation();
+
+    boolean ssPresent = AlignmentUtils
+            .isSecondaryStructurePresent(alignmentAnnotations);
+
+    List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+            pca.isSelected(), ssPresent, (pasimap.isSelected() || pairwise.isSelected()));

 
     /*
      * now we can actually add entries to the combobox,
      * remembering their descriptions for tooltips
      */
 
     /*
      * now we can actually add entries to the combobox,
      * remembering their descriptions for tooltips
      */

-    ScoreModels scoreModels = ScoreModels.getInstance();

     boolean selectedIsPresent = false;
     boolean selectedIsPresent = false;

-    for (ScoreModelI sm : scoreModels.getModels())
+    for (ScoreModelI sm : models)

     {
     {

-      boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-      if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+      if (curSel != null && sm.getName().equals(curSel))

       {
       {

-        if (curSel != null && sm.getName().equals(curSel))
-        {
-          selectedIsPresent = true;
-          curSel = sm.getName();
-        }
-        model.addElement(sm.getName());
-
-        /*
-         * tooltip is description if provided, else text lookup with
-         * fallback on the model name
-         */
-        String tooltip = sm.getDescription();
-        if (tooltip == null)
-        {
-          tooltip = MessageManager.getStringOrReturn("label.score_model_",
-                  sm.getName());
-        }
-        toolTips.add(tooltip);
+        selectedIsPresent = true;
+        curSel = sm.getName();

       }
       }

+      model.addElement(sm.getName());
+
+      /*
+       * tooltip is description if provided, else text lookup with
+       * fallback on the model name
+       */
+      String tooltip = sm.getDescription();
+      if (tooltip == null)
+      {
+        tooltip = MessageManager.getStringOrReturn("label.score_model_",
+                sm.getName());
+      }
+      toolTips.add(tooltip);

     }
     }

+

     if (selectedIsPresent)
     {
       model.setSelectedItem(curSel);
     }
     // finally, update the model
     comboBox.setModel(model);
     if (selectedIsPresent)
     {
       model.setSelectedItem(curSel);
     }
     // finally, update the model
     comboBox.setModel(model);

+    comboBox.setEnabled(model.getSize() > 0);
+
+  }
+
+  /**
+   * Builds a list of score models which are applicable for the alignment and
+   * calculation type (peptide or generic models for protein, nucleotide or
+   * generic models for nucleotide).
+   * <p>
+   * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA.
+   * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62
+   * was the only score matrix supported. This is included if property
+   * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file.
+   * 
+   * @param nucleotide
+   * @param forPca
+   * @param ssPresent
+   *          - include secondary structure similarity model
+   * @param forPasimap
+   *          - limit to ScoreMatrix based models - allows use of AlignSeq
+   * @return
+   */
+  protected static List<ScoreModelI> getApplicableScoreModels(
+          boolean nucleotide, boolean forPca, boolean ssPresent,
+          boolean forPasimap)
+  {
+    List<ScoreModelI> filtered = new ArrayList<>();
+
+    ScoreModels scoreModels = ScoreModels.getInstance();
+    for (ScoreModelI sm : scoreModels.getModels())
+    {
+      if ((!forPasimap || sm instanceof ScoreMatrix)
+              && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
+                      || sm.isSecondaryStructure() && ssPresent))
+
+      {
+        filtered.add(sm);
+      }
+    }
+
+    /*
+     * special case: add BLOSUM62 as last option for nucleotide PCA, 
+     * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+     */
+    if (!forPasimap && nucleotide && forPca
+            && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+    {
+      filtered.add(scoreModels.getBlosum62());
+    }
+
+    return filtered;
+  }
+
+  protected List<String> getApplicableSecondaryStructureSources()
+  {
+    AlignmentAnnotation[] annotations = af.getViewport().getAlignment()
+            .getAlignmentAnnotation();
+
+    List<String> ssSources = AlignmentUtils
+            .getSecondaryStructureSources(annotations);
+    // List<String> ssSources =
+    // AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+
+    return ssSources;

   }
 
   /**
   }
 
   /**

@@ -465,19 +700,67 @@ public class CalculationChooser extends JPanel
   protected void calculate_actionPerformed()
   {
     boolean doPCA = pca.isSelected();
   protected void calculate_actionPerformed()
   {
     boolean doPCA = pca.isSelected();

-    String modelName = modelNames.getSelectedItem().toString();
-    SimilarityParamsI params = getSimilarityParameters(doPCA);
+    boolean doPaSiMap = pasimap.isSelected();
+    boolean doPairwise = pairwise.isSelected();
+    String modelName = modelNames.getSelectedItem() == null ? ""
+            : modelNames.getSelectedItem().toString();
+    String ssSource = "";
+    Object selectedItem = ssSourceDropdown.getSelectedItem();
+    if (selectedItem != null)
+    {
+      ssSource = selectedItem.toString();
+    }
+    SimilarityParams params = getSimilarityParameters(doPCA);
+    if (ssSource.length() > 0)
+    {
+      params.setSecondaryStructureSource(ssSource);
+    }

 
     if (doPCA)
     {
       openPcaPanel(modelName, params);
     }
 
     if (doPCA)
     {
       openPcaPanel(modelName, params);
     }

+    else if (doPaSiMap)
+    {
+      openPasimapPanel(modelName, params);
+    }
+    else if (doPairwise)
+    {
+      openPairwisePanel(modelName, params);
+    }

     else
     {
       openTreePanel(modelName, params);
     }
 
     else
     {
       openTreePanel(modelName, params);
     }
 

-    // closeFrame();
+    closeFrame();
+  }
+
+  private void openPairwisePanel(String modelName, SimilarityParamsI params)
+  {
+    ScoreModelI sm = ScoreModels.getInstance().getScoreModel(modelName,
+            af.alignPanel);
+    if (sm == null || !(sm instanceof ScoreMatrix))
+    {
+      return;
+    }
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        String pairwise_alignment_title = af.formCalculationTitle(
+                MessageManager.getString("action.pairwise_alignment")
+                        + " with " + sm.getName(),
+                af.getViewport().getSelectionGroup() != null,
+                af.getTitle());
+        JInternalFrame frame = new JInternalFrame();
+        frame.setFrameIcon(null);
+        frame.setContentPane(
+                new PairwiseAlignPanel(af.getViewport(), (ScoreMatrix) sm));
+        Desktop.addInternalFrame(frame, pairwise_alignment_title, 600, 500);
+      }
+    }).start();

   }
 
   /**
   }
 
   /**

@@ -539,7 +822,53 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
               JvOptionPane.WARNING_MESSAGE);
       return;
     }

+
+    /*
+     * construct the panel and kick off its calculation thread
+     */

     pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
     pcaPanel = new PCAPanel(af.alignPanel, modelName, params);

+    new Thread(pcaPanel).start();
+
+  }
+
+  /**
+   * Open a new PaSiMap panel on the desktop
+   * 
+   * @param modelName
+   * @param params
+   */
+  protected void openPasimapPanel(String modelName,
+          SimilarityParamsI params)
+  {
+    AlignViewport viewport = af.getViewport();
+
+    /*
+     * gui validation shouldn't allow insufficient sequences here, but leave
+     * this check in in case this method gets exposed programmatically in future
+     */
+    if (((viewport.getSelectionGroup() != null)
+            && (viewport.getSelectionGroup()
+                    .getSize() < MIN_PASIMAP_SELECTION)
+            && (viewport.getSelectionGroup().getSize() > 0))
+            || (viewport.getAlignment()
+                    .getHeight() < MIN_PASIMAP_SELECTION))
+    {
+      JvOptionPane.showInternalMessageDialog(this,
+              MessageManager.formatMessage(
+                      "label.you_need_at_least_n_sequences",
+                      MIN_PASIMAP_SELECTION),
+              MessageManager
+                      .getString("label.sequence_selection_insufficient"),
+              JvOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
+    /*
+     * construct the panel and kick off its calculation thread
+     */
+    pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName);
+    new Thread(pasimapPanel).start();
+

   }
 
   /**
   }
 
   /**

@@ -562,7 +891,7 @@ public class CalculationChooser extends JPanel
    * @param doPCA
    * @return
    */
    * @param doPCA
    * @return
    */

-  protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
+  protected SimilarityParams getSimilarityParameters(boolean doPCA)

   {
     // commented out: parameter choices read from gui widgets
     // SimilarityParamsI params = new SimilarityParams(
   {
     // commented out: parameter choices read from gui widgets
     // SimilarityParamsI params = new SimilarityParams(