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

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index eb4253f..45def89 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -21,7 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -53,6 +53,7 @@ import java.awt.print.PrinterException;
 import java.awt.print.PrinterJob;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JColorChooser;
@@ -73,15 +74,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   /** DOCUMENT ME!! */
   public static final String PLACEHOLDER = " * ";
 
-  NJTree tree;
+  TreeModel tree;
 
   JScrollPane scrollPane;
 
   TreePanel tp;
 
-  AlignViewport av;
+  private AlignViewport av;
 
-  AlignmentPanel ap;
+  private AlignmentPanel ap;
 
   Font font;
 
@@ -99,7 +100,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   int offy;
 
-  float threshold;
+  private float threshold;
 
   String longestName;
 
@@ -129,7 +130,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   {
     this.tp = tp;
     this.av = ap.av;
-    this.ap = ap;
+    this.setAssociatedPanel(ap);
     font = av.getFont();
     scrollPane = scroller;
     addMouseListener(this);
@@ -168,7 +169,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setTree(NJTree tree)
+  public void setTree(TreeModel tree)
   {
     this.tree = tree;
     tree.findHeight(tree.getTopNode());
@@ -278,8 +279,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
-              .getName()) : node.getName();
+      String name = (markPlaceholders && node.isPlaceholder())
+              ? (PLACEHOLDER + node.getName())
+              : node.getName();
 
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = font.getSize();
@@ -331,9 +333,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g.fillRect(xend - 2, ypos - 2, 4, 4);
       }
 
-      int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
-              + offy;
-      int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+      int ystart = (node.left() == null ? 0
+              : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy;
+      int yend = (node.right() == null ? 0
+              : (int) (((SequenceNode) node.right()).ycount * chunk))
               + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
@@ -422,8 +425,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     SequenceNode top = tree.getTopNode();
 
-    double wscale = ((width * .8) - (offx * 2))
-            / tree.getMaxHeight();
+    double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight();
 
     if (top.count == 0)
     {
@@ -549,7 +551,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
-    PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+    PageFormat defaultPage = printJob.defaultPage();
+    PageFormat pf = printJob.pageDialog(defaultPage);
+
+    if (defaultPage == pf)
+    {
+      /*
+       * user cancelled
+       */
+      return;
+    }
 
     printJob.setPrintable(this, pf);
 
@@ -643,8 +654,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     if (tree == null)
     {
-      g.drawString(MessageManager.getString("label.calculating_tree")
-              + "....", 20, getHeight() / 2);
+      g.drawString(
+              MessageManager.getString("label.calculating_tree") + "....",
+              20, getHeight() / 2);
     }
     else
     {
@@ -655,9 +667,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         repaint();
       }
 
-      if (fitToWindow
-              || (!fitToWindow && (scrollPane.getHeight() > ((fm
-                      .getHeight() * nameHash.size()) + offy))))
+      if (fitToWindow || (!fitToWindow && (scrollPane
+              .getHeight() > ((fm.getHeight() * nameHash.size()) + offy))))
       {
         draw(g, scrollPane.getWidth(), scrollPane.getHeight());
         setPreferredSize(null);
@@ -741,7 +752,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g2.setColor(Color.gray);
       }
 
-      int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
+      int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx)))
+              + offx);
 
       g2.drawLine(x, 0, x, getHeight());
     }
@@ -835,7 +847,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (col != null)
     {
       setColor(highlightNode, col);
-      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
       repaint();
     }
   }
@@ -850,8 +862,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (ob instanceof SequenceNode)
     {
       highlightNode = (SequenceNode) ob;
-      this.setToolTipText("<html>"
-              + MessageManager.getString("label.highlightnode"));
+      this.setToolTipText(
+              "<html>" + MessageManager.getString("label.highlightnode"));
       repaint();
 
     }
@@ -916,7 +928,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (ob instanceof SequenceI)
     {
       treeSelectionChanged((Sequence) ob);
-      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
       repaint();
       av.sendSelection();
       return;
@@ -929,8 +941,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         threshold = (float) (x - offx)
                 / (float) (getWidth() - labelLength - (2 * offx));
 
-        tree.getGroups().removeAllElements();
-        tree.groupNodes(tree.getTopNode(), threshold);
+        List<SequenceNode> groups = tree.groupNodes(threshold);
         setColor(tree.getTopNode(), Color.black);
 
         AlignmentPanel[] aps = getAssociatedPanels();
@@ -950,28 +961,36 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             aps[a].av.getCodingComplement().clearSequenceColours();
           }
         }
-        colourGroups();
+        colourGroups(groups);
+
+        /*
+         * clear partition (don't show vertical line) if
+         * it is to the right of all nodes
+         */
+        if (groups.isEmpty())
+        {
+          threshold = 0f;
+        }
       }
 
-      PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
+      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
       repaint();
     }
 
   }
 
-  void colourGroups()
+  void colourGroups(List<SequenceNode> groups)
   {
     AlignmentPanel[] aps = getAssociatedPanels();
-    for (int i = 0; i < tree.getGroups().size(); i++)
+    for (int i = 0; i < groups.size(); i++)
     {
       Color col = new Color((int) (Math.random() * 255),
               (int) (Math.random() * 255), (int) (Math.random() * 255));
-      setColor(tree.getGroups().elementAt(i), col.brighter());
+      setColor(groups.get(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
-              .elementAt(i));
+      Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
 
-      Vector<SequenceI> sequences = new Vector<SequenceI>();
+      Vector<SequenceI> sequences = new Vector<>();
 
       for (int j = 0; j < l.size(); j++)
       {
@@ -998,9 +1017,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColourScheme(sg,
-                  ColourSchemeProperty.getColourName(av
-                          .getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+                  .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
         // if (cs != null)
@@ -1020,8 +1038,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       for (int a = 0; a < aps.length; a++)
       {
         if (aps[a].av.getGlobalColourScheme() != null
-                && aps[a].av.getResidueShading()
-                        .conservationApplied())
+                && aps[a].av.getResidueShading().conservationApplied())
         {
           Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes());
@@ -1110,7 +1127,37 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      return new AlignmentPanel[] { ap };
+      return new AlignmentPanel[] { getAssociatedPanel() };
     }
   }
+
+  public AlignmentPanel getAssociatedPanel()
+  {
+    return ap;
+  }
+
+  public void setAssociatedPanel(AlignmentPanel ap)
+  {
+    this.ap = ap;
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public void setViewport(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public float getThreshold()
+  {
+    return threshold;
+  }
+
+  public void setThreshold(float threshold)
+  {
+    this.threshold = threshold;
+  }
 }