*/
package jalview.io.vamsas;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
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);
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();