X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCalculationChooser.java;h=ae92168884495ec933771c24ae68eeeff623110f;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=b97357287849c3d774909a103e98f8e2c2852aa0;hpb=45cc7240488ccc4ec95bdcef7f681dd703a76a85;p=jalview.git

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index b973572..ae92168 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -27,6 +27,7 @@ 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.ext.archaeopteryx.AptxInit;
 import jalview.util.MessageManager;
@@ -64,8 +65,6 @@ import javax.swing.JRadioButton;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
-import org.forester.io.parsers.nhx.NHXParser;
-
 /**
  * A dialog where a user can choose and action Tree or PCA calculation options
  */
@@ -161,12 +160,15 @@ 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);
@@ -175,8 +177,8 @@ public class CalculationChooser extends JPanel
     JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
     treePanel.setOpaque(false);
 
-    treePanel.setBorder(BorderFactory
-            .createTitledBorder(MessageManager.getString("label.tree")));
+    JvSwingUtils.createTitledBorder(treePanel,
+            MessageManager.getString("label.tree"), true);
 
     // then copy the inset dimensions for the border-less PCA panel
     JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));
@@ -276,9 +278,9 @@ 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);
@@ -296,6 +298,7 @@ public class CalculationChooser extends JPanel
       };
     });
 
+    validateCalcTypes();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
@@ -425,38 +428,40 @@ public class CalculationChooser extends JPanel
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
     DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+    /*
+     * select the score models applicable to the alignment type
+     */
+    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+    List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+            pca.isSelected());
 
     /*
      * now we can actually add entries to the combobox,
      * remembering their descriptions for tooltips
      */
-    ScoreModels scoreModels = ScoreModels.getInstance();
     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);
@@ -466,6 +471,47 @@ public class CalculationChooser extends JPanel
   }
 
   /**
+   * 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
+   * @return
+   */
+  protected static List<ScoreModelI> getApplicableScoreModels(
+          boolean nucleotide, boolean forPca)
+  {
+    List<ScoreModelI> filtered = new ArrayList<>();
+
+    ScoreModels scoreModels = ScoreModels.getInstance();
+    for (ScoreModelI sm : scoreModels.getModels())
+    {
+      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+      {
+        filtered.add(sm);
+      }
+    }
+
+    /*
+     * special case: add BLOSUM62 as last option for nucleotide PCA, 
+     * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+     */
+    if (nucleotide && forPca
+            && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+    {
+      filtered.add(scoreModels.getBlosum62());
+    }
+
+    return filtered;
+  }
+
+  /**
    * Open and calculate the selected tree or PCA on 'OK'
    * 
    * @throws IOException
@@ -516,7 +562,7 @@ public class CalculationChooser extends JPanel
             tree.getTopNode());
     String output = newick.print(tree.hasBootstrap(), tree.hasDistances(),
             tree.hasRootDistance());
-    AptxInit.createInstances(af.getTitle(), output, new NHXParser(),
+    AptxInit.createInstanceFromNhx(af.getTitle(), output, 
             af.getViewport());
     // openTreePanel(tree, treeAlgo, substitutionMatrix);
   }
@@ -594,7 +640,13 @@ 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();
+
   }
 
   /**