package jalview.ext.archaeopteryx;
import jalview.datamodel.SequenceI;
+import jalview.ext.forester.DataConversions;
import jalview.ext.treeviewer.TreeNodeI;
import java.awt.Color;
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() != null)
+ {
+ nodeSeq = DataConversions
+ .createJalviewSequence(aptxNode);
+ }
originalNodes.put(aptxNode, this);
wrappedNodes.put(this, aptxNode);
public SequenceI getSequence()
{
return nodeSeq;
- // ideally this would return a converted node.getNodeData().getSequence()
}
@Override
@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();
+ }
+
}