Merge branch 'documentation/JAL-2418_release2102' 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 f784fb0..d800d20 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -20,7 +20,7 @@
  */
 package jalview.io.vamsas;
 
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
 import jalview.analysis.TreeModel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -220,15 +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);
@@ -240,12 +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(NJTree.NEIGHBOUR_JOINING);
+      prov.getEntry(0).getParam(0)
+              .setContent(TreeBuilder.NEIGHBOUR_JOINING);
       // TODO: type of tree is a general parameter
-      int ranges[] = tp.getTree().seqData.getVisibleContigs();
+      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();