JAL-4134 compute normalised dot product for contact matrix similarities

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 40cf080..a1bcebd 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -50,6 +50,7 @@ import javax.swing.ToolTipManager;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -106,9 +107,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   Map<Object, Rectangle> nameHash = new Hashtable<>();
 
-  Map<SequenceNode, Rectangle> nodeHash = new Hashtable<>();
+  Map<BinaryNode, Rectangle> nodeHash = new Hashtable<>();
 
-  SequenceNode highlightNode;
+  BinaryNode highlightNode;
 
   boolean applyToAllViews = false;
 
@@ -173,15 +174,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     tree.findHeight(tree.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+    Vector<BinaryNode> leaves = tree.findLeaves(tree.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
     for (int i = 0; i < leaves.size(); i++)
     {
-      SequenceNode lf = leaves.elementAt(i);
+      BinaryNode lf = leaves.elementAt(i);
 
-      if (lf.isPlaceholder())
+      if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
       {
         has_placeholders = true;
       }
@@ -215,7 +216,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param offy
    *          DOCUMENT ME!
    */
-  public void drawNode(Graphics g, SequenceNode node, float chunk,
+  public void drawNode(Graphics g, BinaryNode node, float chunk,
           double wscale, int width, int offx, int offy)
   {
     if (node == null)
@@ -259,7 +260,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       if (showDistances && (node.dist > 0))
       {
-        nodeLabel = new Format("%-.2f").form(node.dist);
+        nodeLabel = new Format("%g").form(node.dist);
       }
 
       if (showBootstrap && node.bootstrap > -1)
@@ -277,7 +278,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder())
+      String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
               ? (PLACEHOLDER + node.getName())
               : node.getName();
 
@@ -306,9 +307,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx,
+      drawNode(g, (BinaryNode) node.left(), chunk, wscale, width, offx,
               offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx,
+      drawNode(g, (BinaryNode) node.right(), chunk, wscale, width, offx,
               offy);
 
       double height = node.height;
@@ -332,9 +333,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
 
       int ystart = (node.left() == null ? 0
-              : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy;
+              : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
       int yend = (node.right() == null ? 0
-              : (int) (((SequenceNode) node.right()).ycount * chunk))
+              : (int) (((BinaryNode) node.right()).ycount * chunk))
               + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
@@ -347,7 +348,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       if (showDistances && (node.dist > 0))
       {
-        nodeLabel = new Format("%-.2f").form(node.dist);
+        nodeLabel = new Format("%g").form(node.dist);
       }
 
       if (showBootstrap && node.bootstrap > -1)
@@ -390,7 +391,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
     }
 
-    for (Entry<SequenceNode, Rectangle> entry : nodeHash.entrySet())
+    for (Entry<BinaryNode, Rectangle> entry : nodeHash.entrySet())
     {
       Rectangle rect = entry.getValue();
 
@@ -415,14 +416,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     int width = getWidth();
     int height = getHeight();
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight();
 
     if (top.count == 0)
     {
-      top.count = ((SequenceNode) top.left()).count
-              + ((SequenceNode) top.right()).count;
+      top.count = ((BinaryNode) top.left()).count
+              + ((BinaryNode) top.right()).count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;
@@ -448,7 +449,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param offy
    *          DOCUMENT ME!
    */
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+  public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,
           double wscale, int width, int offx, int offy)
   {
     if (node == null)
@@ -459,8 +460,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if ((node.left() == null) && (node.right() == null))
     {
       double height = node.height;
-//      double dist = node.dist;
-//      int xstart = (int) ((height - dist) * wscale) + offx;
+      // double dist = node.dist;
+      // int xstart = (int) ((height - dist) * wscale) + offx;
       int xend = (int) (height * wscale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
@@ -481,9 +482,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width,
+      pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width,
               offx, offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width,
+      pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width,
               offx, offy);
     }
   }
@@ -496,7 +497,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param c
    *          DOCUMENT ME!
    */
-  public void setColor(SequenceNode node, Color c)
+  public void setColor(BinaryNode node, Color c)
   {
     if (node == null)
     {
@@ -516,8 +517,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
       }
     }
-    setColor((SequenceNode) node.left(), c);
-    setColor((SequenceNode) node.right(), c);
+    setColor((BinaryNode) node.left(), c);
+    setColor((BinaryNode) node.right(), c);
   }
 
   /**
@@ -713,12 +714,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     double wscale = (width - labelLength - (offx * 2))
             / tree.getMaxHeight();
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     if (top.count == 0)
     {
-      top.count = ((SequenceNode) top.left()).count
-              + ((SequenceNode) top.right()).count;
+      top.count = ((BinaryNode) top.left()).count
+              + ((BinaryNode) top.right()).count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;
@@ -804,7 +805,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
+      Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
 
       for (int i = 0; i < leaves.size(); i++)
       {
@@ -826,7 +827,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   void chooseSubtreeColour()
   {
     String ttl = MessageManager.getString("label.select_subtree_colour");
-    ColourChooserListener listener = new ColourChooserListener() {
+    ColourChooserListener listener = new ColourChooserListener()
+    {
       @Override
       public void colourSelected(Color c)
       {
@@ -835,7 +837,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         repaint();
       }
     };
-    JalviewColourChooser.showColourChooser(this, ttl,  highlightNode.color, listener);
+    JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color,
+            listener);
   }
 
   @Override
@@ -845,9 +848,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     Object ob = findElement(evt.getX(), evt.getY());
 
-    if (ob instanceof SequenceNode)
+    if (ob instanceof BinaryNode)
     {
-      highlightNode = (SequenceNode) ob;
+      highlightNode = (BinaryNode) ob;
       this.setToolTipText(
               "<html>" + MessageManager.getString("label.highlightnode"));
       repaint();
@@ -914,12 +917,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (ob instanceof SequenceI)
     {
       treeSelectionChanged((Sequence) ob);
-      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
+      PaintRefresher.Refresh(tp,
+              getAssociatedPanel().av.getSequenceSetId());
       repaint();
       av.sendSelection();
       return;
     }
-    else if (!(ob instanceof SequenceNode))
+    else if (!(ob instanceof BinaryNode))
     {
       // Find threshold
       if (tree.getMaxHeight() != 0)
@@ -927,7 +931,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         threshold = (float) (x - offx)
                 / (float) (getWidth() - labelLength - (2 * offx));
 
-        List<SequenceNode> groups = tree.groupNodes(threshold);
+        List<BinaryNode> groups = tree.groupNodes(threshold);
         setColor(tree.getTopNode(), Color.black);
 
         AlignmentPanel[] aps = getAssociatedPanels();
@@ -960,13 +964,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
       }
 
-      PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
+      PaintRefresher.Refresh(tp,
+              getAssociatedPanel().av.getSequenceSetId());
       repaint();
     }
 
   }
 
-  void colourGroups(List<SequenceNode> groups)
+  void colourGroups(List<BinaryNode> groups)
   {
     AlignmentPanel[] aps = getAssociatedPanels();
     for (int i = 0; i < groups.size(); i++)
@@ -975,7 +980,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
               (int) (Math.random() * 255), (int) (Math.random() * 255));
       setColor(groups.get(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
+      Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
 
       Vector<SequenceI> sequences = new Vector<>();