JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)

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

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 8a95594..183419e 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -105,6 +105,11 @@ public class CalculationChooser extends JPanel
 
   List<String> tips = new ArrayList<String>();
 
+  /*
+   * the most recently opened PCA results panel
+   */
+  private PCAPanel pcaPanel;
+
   /**
    * Constructor
    * 
@@ -164,14 +169,14 @@ 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));
     Insets b = treePanel.getBorder().getBorderInsets(treePanel);
-    pcaBorderless.setBorder(BorderFactory.createEmptyBorder(2, b.left, 2,
-            b.right));
+    pcaBorderless.setBorder(
+            BorderFactory.createEmptyBorder(2, b.left, 2, b.right));
     pcaBorderless.setOpaque(false);
 
     pcaBorderless.add(pca, FlowLayout.LEFT);
@@ -186,7 +191,7 @@ public class CalculationChooser extends JPanel
     calcTypes.add(pca);
     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);
-    
+
     ActionListener calcChanged = new ActionListener()
     {
       @Override
@@ -265,9 +270,9 @@ 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);
@@ -335,8 +340,8 @@ public class CalculationChooser extends JPanel
    */
   private boolean checkEnabled(JRadioButton calc, int size, int minsize)
   {
-    String ttip = MessageManager.formatMessage(
-            "label.you_need_at_least_n_sequences", minsize);
+    String ttip = MessageManager
+            .formatMessage("label.you_need_at_least_n_sequences", minsize);
 
     calc.setEnabled(size >= minsize);
     if (!calc.isEnabled())
@@ -383,7 +388,8 @@ public class CalculationChooser extends JPanel
       @Override
       public void mouseEntered(MouseEvent e)
       {
-        scoreModelsCombo.setToolTipText(tips.get(scoreModelsCombo.getSelectedIndex()));
+        scoreModelsCombo.setToolTipText(
+                tips.get(scoreModelsCombo.getSelectedIndex()));
       }
 
       @Override
@@ -490,19 +496,17 @@ public class CalculationChooser extends JPanel
     SequenceGroup sg = viewport.getSelectionGroup();
     if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
     {
-      JvOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-              .formatMessage("label.you_need_at_least_n_sequences",
+      JvOptionPane.showMessageDialog(Desktop.desktop,
+              MessageManager.formatMessage(
+                      "label.you_need_at_least_n_sequences",
                       MIN_TREE_SELECTION),
-                      MessageManager
-                              .getString("label.not_enough_sequences"),
-                      JvOptionPane.WARNING_MESSAGE);
+              MessageManager.getString("label.not_enough_sequences"),
+              JvOptionPane.WARNING_MESSAGE);
       return;
     }
 
-    String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
+    String treeType = neighbourJoining.isSelected()
+            ? TreeBuilder.NEIGHBOUR_JOINING
             : TreeBuilder.AVERAGE_DISTANCE;
     af.newTreePanel(treeType, modelName, params);
   }
@@ -522,18 +526,20 @@ public class CalculationChooser extends JPanel
      * this check in in case this method gets exposed programmatically in future
      */
     if (((viewport.getSelectionGroup() != null)
-            && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) && (viewport
-            .getSelectionGroup().getSize() > 0))
+            && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION)
+            && (viewport.getSelectionGroup().getSize() > 0))
             || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION))
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.you_need_at_least_n_sequences",
-                      MIN_PCA_SELECTION), MessageManager
-              .getString("label.sequence_selection_insufficient"),
+      JvOptionPane.showInternalMessageDialog(this,
+              MessageManager.formatMessage(
+                      "label.you_need_at_least_n_sequences",
+                      MIN_PCA_SELECTION),
+              MessageManager
+                      .getString("label.sequence_selection_insufficient"),
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -575,7 +581,8 @@ public class CalculationChooser extends JPanel
      */
     boolean matchGap = doPCA ? false : treeMatchGaps;
 
-    return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
+    return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
+            matchOnShortestLength);
   }
 
   /**
@@ -590,4 +597,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }