JAL-1551 spotless

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

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 48e9d64..f965ff4 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 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;
@@ -51,8 +52,8 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
-public class TreeCanvas extends Panel implements MouseListener,
-        MouseMotionListener
+public class TreeCanvas extends Panel
+        implements MouseListener, MouseMotionListener
 {
   TreeModel tree;
 
@@ -86,7 +87,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
   Hashtable nodeHash = new Hashtable();
 
-  SequenceNode highlightNode;
+  BinaryNode highlightNode;
 
   AlignmentPanel ap;
 
@@ -122,15 +123,15 @@ public class TreeCanvas extends Panel implements MouseListener,
     tree2.findHeight(tree2.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector<SequenceNode> leaves = tree2.findLeaves(tree2.getTopNode());
+    Vector<BinaryNode> leaves = tree2.findLeaves(tree2.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;
       }
@@ -146,7 +147,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     setMarkPlaceholders(has_placeholders);
   }
 
-  public void drawNode(Graphics g, SequenceNode node, float chunk,
+  public void drawNode(Graphics g, BinaryNode node, float chunk,
           double scale, int width, int offx, int offy)
   {
     if (node == null)
@@ -210,8 +211,10 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
-              .getName()) : node.getName();
+      String name = (markPlaceholders && node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())
+                      ? (PLACEHOLDER + node.getName())
+                      : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
@@ -236,9 +239,9 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
     else
     {
-      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+      drawNode(g, (BinaryNode) node.left(), chunk, scale, width, offx,
               offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+      drawNode(g, (BinaryNode) node.right(), chunk, scale, width, offx,
               offy);
 
       double height = node.height;
@@ -261,10 +264,10 @@ public class TreeCanvas extends Panel implements MouseListener,
         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)
-              + offy;
+      int ystart = (int) (node.left() == null ? 0
+              : (((BinaryNode) node.left()).ycount * chunk)) + offy;
+      int yend = (int) (node.right() == null ? 0
+              : (((BinaryNode) node.right()).ycount * chunk)) + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
@@ -337,20 +340,20 @@ public class TreeCanvas extends Panel implements MouseListener,
     int width = getSize().width;
     int height = getSize().height;
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     double wscale = (float) (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;
 
     pickNode(pickBox, top, chunk, wscale, width, offx, offy);
   }
 
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+  public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,
           double scale, int width, int offx, int offy)
   {
     if (node == null)
@@ -383,14 +386,14 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
     else
     {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
-              offx, offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+      pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx,
+              offy);
+      pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width,
               offx, offy);
     }
   }
 
-  public void setColor(SequenceNode node, Color c)
+  public void setColor(BinaryNode node, Color c)
   {
     if (node == null)
     {
@@ -409,8 +412,8 @@ public class TreeCanvas extends Panel implements MouseListener,
     else
     {
       node.color = c;
-      setColor((SequenceNode) node.left(), c);
-      setColor((SequenceNode) node.right(), c);
+      setColor((BinaryNode) node.left(), c);
+      setColor((BinaryNode) node.right(), c);
     }
   }
 
@@ -468,12 +471,12 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     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;
 
@@ -490,7 +493,8 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.setColor(Color.gray);
       }
 
-      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
+      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx)
+              + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
@@ -525,7 +529,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       }
       else
       {
-        Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
+        Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
 
         for (int i = 0; i < leaves.size(); i++)
         {
@@ -552,9 +556,9 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     Object ob = findElement(evt.getX(), evt.getY());
 
-    if (ob instanceof SequenceNode)
+    if (ob instanceof BinaryNode)
     {
-      highlightNode = (SequenceNode) ob;
+      highlightNode = (BinaryNode) ob;
       repaint();
     }
     else
@@ -594,7 +598,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         threshold = (float) (x - offx)
                 / (float) (getSize().width - labelLength - 2 * offx);
 
-        List<SequenceNode> groups = tree.groupNodes(threshold);
+        List<BinaryNode> groups = tree.groupNodes(threshold);
         setColor(tree.getTopNode(), Color.black);
 
         av.setSelectionGroup(null);
@@ -618,7 +622,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
   }
 
-  void colourGroups(List<SequenceNode> groups)
+  void colourGroups(List<BinaryNode> groups)
   {
     for (int i = 0; i < groups.size(); i++)
     {
@@ -627,9 +631,9 @@ public class TreeCanvas extends Panel implements MouseListener,
               (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<SequenceI>();
+      Vector<SequenceI> sequences = new Vector<>();
       for (int j = 0; j < l.size(); j++)
       {
         SequenceI s1 = (SequenceI) l.elementAt(j).element();
@@ -655,9 +659,9 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColourScheme(sg,
-                  ColourSchemeProperty.getColourName(av
-                          .getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(av, sg,
+                  ColourSchemeProperty
+                          .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
         // if (cs != null)