/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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;
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
+ prov.getEntry(0).getParam(0)
+ .setContent(TreeBuilder.NEIGHBOUR_JOINING);
+ // TODO: type of tree is a general parameter
int ranges[] = tp.getTree().seqData.getVisibleContigs();
// VisibleContigs are with respect to alignment coordinates. Still need
// offsets
}
}
if (alsq.size() < sequences.length)
+ {
Cache.log
.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+ }
return alsq;
}
public void UpdateSequenceTreeMap(TreePanel tp)
{
if (tp == null || tree == null)
+ {
return;
- Vector leaves = new Vector();
+ }
+
if (tp.getTree() == null)
{
Cache.log.warn("Not updating SequenceTreeMap for "
+ tree.getVorbaId());
return;
}
- tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+ Vector<SequenceNode> leaves = tp.getTree().findLeaves(
+ tp.getTree().getTopNode());
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
int sz = tn.length;
/**
* 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 leaves = new Vector();
- ntree.findLeaves(ntree.getTopNode(), leaves);
+ Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
+ .getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
--occurence;
}
else
+ {
bn = null;
+ }
}
return bn;
}
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));