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JAL-2428 separate TreeModel from TreeBuilder/NJTree/AverageDistanceTree
[jalview.git]
/
src
/
jalview
/
io
/
vamsas
/
Tree.java
diff --git
a/src/jalview/io/vamsas/Tree.java
b/src/jalview/io/vamsas/Tree.java
index
89877e2
..
f784fb0
100644
(file)
--- a/
src/jalview/io/vamsas/Tree.java
+++ b/
src/jalview/io/vamsas/Tree.java
@@
-21,6
+21,7
@@
package jalview.io.vamsas;
import jalview.analysis.NJTree;
package jalview.io.vamsas;
import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
@@
-370,13
+371,14
@@
public class Tree extends DatastoreItem
/**
* construct treenode mappings for mapped sequences
*
/**
* construct treenode mappings for mapped sequences
*
- * @param ntree
+ * @param treeModel
* @param newick
* @return
*/
* @param newick
* @return
*/
- public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
+ public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
{
{
- Vector<SequenceNode> leaves = ntree.findLeaves(ntree.getTopNode());
+ Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
+ .getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
@@
-496,7
+498,7
@@
public class Tree extends DatastoreItem
bindjvvobj(tp, tree);
tree.setTitle(tp.getTitle());
Newick newick = new Newick();
bindjvvobj(tp, tree);
tree.setTitle(tp.getTitle());
Newick newick = new Newick();
- newick.setContent(tp.getTree().toString());
+ newick.setContent(tp.getTree().print());
newick.setTitle(tp.getTitle());
tree.addNewick(newick);
tree.setProvenance(makeTreeProvenance(jal, tp));
newick.setTitle(tp.getTitle());
tree.addNewick(newick);
tree.setProvenance(makeTreeProvenance(jal, tp));