import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
}
} catch (Exception e)
{
- Cache.log.warn("Problems parsing treefile '"
+ Console.warn("Problems parsing treefile '"
+ tree.getNewick(0).getContent() + "'", e);
}
}
@Override
public void conflict()
{
- Cache.log.info(
+ Console.info(
"Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
}
* idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
* getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
* title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
- * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+ * (Exception e) { Cache.warn("Problems parsing treefile '" +
* tree.getNewick(0).getContent() + "'", e); }
*/
log.debug("Update the local tree in jalview from the document.");
*/
private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
{
- Cache.log.debug("Making Tree provenance for " + tp.getTitle());
+ Console.debug("Making Tree provenance for " + tp.getTitle());
Provenance prov = new Provenance();
prov.addEntry(new Entry());
prov.getEntry(0).setAction("imported " + tp.getTitle());
vInput.addSeg(visSeg);
}
}
- Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
+ Console.debug("Finished Tree provenance for " + tp.getTitle());
return prov;
}
}
if (alsq.size() < sequences.length)
{
- Cache.log.warn(
+ Console.warn(
"Not recovered all alignment sequences for given set of input sequence CIGARS");
}
return alsq;
if (tp.getTree() == null)
{
- Cache.log.warn(
- "Not updating SequenceTreeMap for " + tree.getVorbaId());
+ Console.warn("Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
- Vector<SequenceNode> leaves = tp.getTree()
+ Vector<BinaryNode> leaves = tp.getTree()
.findLeaves(tp.getTree().getTopNode());
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
*/
public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
{
- Vector<SequenceNode> leaves = treeModel
+ Vector<BinaryNode> leaves = treeModel
.findLeaves(treeModel.getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
{
if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
{
- Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
- .element();
+ Object assocseq = ((BinaryNode) tnode).element();
if (assocseq instanceof SequenceI)
{
Vobject vobj = this.getjv2vObj(assocseq);
Integer nindx = (Integer) nodespecs.get(nname);
if (nindx == null)
{
- nindx = new Integer(1);
+ nindx = Integer.valueOf(1);
}
nname = nindx.toString() + " " + nname;
return nname;
String oval = nodespec.substring(0, nodespec.indexOf(' '));
try
{
- occurence = new Integer(oval).intValue();
+ occurence = Integer.valueOf(oval).intValue();
} catch (Exception e)
{
System.err.println("Invalid nodespec '" + nodespec + "'");
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Cache.log.warn(
- "Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
+ Console.warn("Ignoring additional input spec in provenance entry "
+ + tp.getEntry(pe).toString());
}
// LATER: deal sensibly with multiple inputs
Input vInput = tp.getEntry(pe).getInput(0);
// bidirection alignments yet.
if (to < se[1])
{
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
+ Console.warn("Ignoring invalid segment in InputData spec.");
}
else
{
return new Object[] { new AlignmentView(view), jal };
}
}
- Cache.log.debug(
+ Console.debug(
"Returning null for input data recovery from provenance.");
return null;
}
return true;
} catch (Exception e)
{
- Cache.log.debug("Failed to parse newick tree string", e);
+ Console.debug("Failed to parse newick tree string", e);
}
return false;
}