JAL-2446 merged to spike branch

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 84fd82f..e60ac8e 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;
@@ -73,7 +74,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   /** DOCUMENT ME!! */
   public static final String PLACEHOLDER = " * ";
 
-  NJTree tree;
+  TreeModel tree;
 
   JScrollPane scrollPane;
 
@@ -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());
@@ -207,7 +208,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    *          DOCUMENT ME!
    * @param chunk
    *          DOCUMENT ME!
-   * @param scale
+   * @param wscale
    *          DOCUMENT ME!
    * @param width
    *          DOCUMENT ME!
@@ -217,7 +218,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    *          DOCUMENT ME!
    */
   public void drawNode(Graphics g, SequenceNode node, float chunk,
-          float scale, int width, int offx, int offy)
+          double wscale, int width, int offx, int offy)
   {
     if (node == null)
     {
@@ -227,11 +228,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if ((node.left() == null) && (node.right() == null))
     {
       // Drawing leaf node
-      float height = node.height;
-      float dist = node.dist;
+      double height = node.height;
+      double dist = node.dist;
 
-      int xstart = (int) ((height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
+      int xstart = (int) ((height - dist) * wscale) + offx;
+      int xend = (int) (height * wscale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
 
@@ -306,16 +307,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+      drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx,
               offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+      drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx,
               offy);
 
-      float height = node.height;
-      float dist = node.dist;
+      double height = node.height;
+      double dist = node.dist;
 
-      int xstart = (int) ((height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
+      int xstart = (int) ((height - dist) * wscale) + offx;
+      int xend = (int) (height * wscale) + offx;
       int ypos = (int) (node.ycount * chunk) + offy;
 
       g.setColor(node.color.darker());
@@ -331,16 +332,17 @@ 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);
       nodeHash.put(node, pos);
 
-      g.drawLine((int) (height * scale) + offx, ystart,
-              (int) (height * scale) + offx, yend);
+      g.drawLine((int) (height * wscale) + offx, ystart,
+              (int) (height * wscale) + offx, yend);
 
       String nodeLabel = "";
 
@@ -422,7 +424,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     SequenceNode top = tree.getTopNode();
 
-    float wscale = (float) ((width * .8) - (offx * 2))
+    double wscale = ((width * .8) - (offx * 2))
             / tree.getMaxHeight();
 
     if (top.count == 0)
@@ -445,7 +447,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    *          DOCUMENT ME!
    * @param chunk
    *          DOCUMENT ME!
-   * @param scale
+   * @param wscale
    *          DOCUMENT ME!
    * @param width
    *          DOCUMENT ME!
@@ -455,7 +457,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    *          DOCUMENT ME!
    */
   public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
-          float scale, int width, int offx, int offy)
+          double wscale, int width, int offx, int offy)
   {
     if (node == null)
     {
@@ -464,11 +466,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     if ((node.left() == null) && (node.right() == null))
     {
-      float height = node.height;
-      float dist = node.dist;
+      double height = node.height;
+      double dist = node.dist;
 
-      int xstart = (int) ((height - dist) * scale) + offx;
-      int xend = (int) (height * scale) + offx;
+      int xstart = (int) ((height - dist) * wscale) + offx;
+      int xend = (int) (height * wscale) + offx;
 
       int ypos = (int) (node.ycount * chunk) + offy;
 
@@ -488,9 +490,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+      pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width,
               offx, offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+      pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width,
               offx, offy);
     }
   }
@@ -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);
 
@@ -715,7 +726,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
 
-    float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight();
+    double wscale = (width - labelLength - (offx * 2))
+            / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
@@ -928,8 +940,7 @@ 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();
@@ -949,7 +960,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             aps[a].av.getCodingComplement().clearSequenceColours();
           }
         }
-        colourGroups();
+        colourGroups(groups);
       }
 
       PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
@@ -958,17 +969,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   }
 
-  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>();
 
@@ -997,17 +1007,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
-                  .getColourName(av.getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(sg,
+                  ColourSchemeProperty.getColourName(av
+                          .getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs != null)
-        {
-          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.isIgnoreGapsConsensus());
-        }
+        // if (cs != null)
+        // {
+        // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+        // av.isIgnoreGapsConsensus());
+        // }
       }
-      sg.cs = cs;
+      sg.setColourScheme(cs);
+      sg.getGroupColourScheme().setThreshold(
+              av.getResidueShading().getThreshold(),
+              av.isIgnoreGapsConsensus());
       // sg.recalcConservation();
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -1015,7 +1029,8 @@ 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.getGlobalColourScheme().conservationApplied())
+                && aps[a].av.getResidueShading()
+                        .conservationApplied())
         {
           Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes());