Merge branch 'features/JAL-2393customMatrices' into develop

[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 a3781a7..d800d20 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -20,7 +20,8 @@
  */
 package jalview.io.vamsas;
 
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -219,15 +220,17 @@ public class Tree extends DatastoreItem
     prov.getEntry(0).setUser(provEntry.getUser());
     prov.getEntry(0).setApp(provEntry.getApp());
     prov.getEntry(0).setDate(provEntry.getDate());
-    if (tp.getTree().hasOriginalSequenceData())
+
+    AlignmentView originalData = tp.getTree().getOriginalData();
+    if (originalData != null)
     {
       Input vInput = new Input();
       // LATER: check to see if tree input data is contained in this alignment -
       // or just correctly resolve the tree's seqData to the correct alignment
       // in
       // the document.
-      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
-              tp.getTree().seqData.getSequences()));
+      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
+              .getTree().getOriginalData().getSequences()));
       Object[] alsqs = new Object[alsqrefs.size()];
       alsqrefs.copyInto(alsqs);
       vInput.setObjRef(alsqs);
@@ -239,12 +242,13 @@ public class Tree extends DatastoreItem
       prov.getEntry(0).addParam(new Param());
       prov.getEntry(0).getParam(0).setName("treeType");
       prov.getEntry(0).getParam(0).setType("utf8");
-      prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
-      // general parameter
-      int ranges[] = tp.getTree().seqData.getVisibleContigs();
+      prov.getEntry(0).getParam(0)
+              .setContent(TreeBuilder.NEIGHBOUR_JOINING);
+      // TODO: type of tree is a general parameter
+      int ranges[] = originalData.getVisibleContigs();
       // VisibleContigs are with respect to alignment coordinates. Still need
       // offsets
-      int start = tp.getTree().seqData.getAlignmentOrigin();
+      int start = tp.getTree().getOriginalData().getAlignmentOrigin();
       for (int r = 0; r < ranges.length; r += 2)
       {
         Seg visSeg = new Seg();
@@ -370,13 +374,14 @@ public class Tree extends DatastoreItem
   /**
    * construct treenode mappings for mapped sequences
    * 
-   * @param ntree
+   * @param treeModel
    * @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();
@@ -496,7 +501,7 @@ public class Tree extends DatastoreItem
     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));