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;
}
int ystart = (int) (node.left() == null ? 0
- : (((SequenceNode) node.left()).ycount * chunk)) + offy;
+ : (((BinaryNode) node.left()).ycount * chunk)) + offy;
int yend = (int) (node.right() == null ? 0
- : (((SequenceNode) node.right()).ycount * chunk)) + offy;
+ : (((BinaryNode) node.right()).ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
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)
}
else
{
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+ pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width,
offx, offy);
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+ 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)
{
else
{
node.color = c;
- setColor((SequenceNode) node.left(), c);
- setColor((SequenceNode) node.right(), c);
+ setColor((BinaryNode) node.left(), c);
+ setColor((BinaryNode) node.right(), c);
}
}
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;