import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.BranchColor;
public class TreeNode implements TreeNodeI
{
private SequenceI nodeSeq;
private static Map<PhylogenyNode, TreeNodeI> originalNodes = new HashMap<>(
- 500); // prolly make this size dynamic
+ 500); // prolly make this size dynamic?
private static Map<TreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
500);
+ /**
+ * Please don't use me directly.
+ *
+ * @param aptxNode
+ */
private TreeNode(PhylogenyNode aptxNode)
{
node = aptxNode;
- if (!aptxNode.getNodeData().getSequence().isEmpty())
+ if (aptxNode.getNodeData().getSequence() != null)
{
nodeSeq = DataConversions
- .createJalviewSequence(aptxNode.getNodeData().getSequence());
+ .createJalviewSequence(aptxNode);
}
originalNodes.put(aptxNode, this);
wrappedNodes.put(this, aptxNode);
@Override
public void setBranchColor(Color branchColor)
{
- node.getBranchData().setBranchColor(new BranchColor(branchColor));
+ PhylogenyMethods.setBranchColorValue(node, branchColor);
}
return node.getYcoord();
}
+ @Override
+ public boolean isCollapsed()
+ {
+ return node.isCollapse();
+ }
+
}