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;
}
* @return vector of alignment sequences in order of SeqCigar array (but
* missing unfound seqcigars)
*/
- private Vector findAlignmentSequences(AlignmentI jal,
+ private Vector<SequenceI> findAlignmentSequences(AlignmentI jal,
SeqCigar[] sequences)
{
SeqCigar[] tseqs = new SeqCigar[sequences.length];
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
- Vector alsq = new Vector();
- List<SequenceI> jalsqs;
- synchronized (jalsqs = jal.getSequences())
+ Vector<SequenceI> alsq = new Vector<>();
+ List<SequenceI> jalsqs = jal.getSequences();
+ synchronized (jalsqs)
{
for (SequenceI asq : jalsqs)
{
}
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
}
if (jvseq instanceof SequenceI)
{
- leaf.setElement(jvseq);
+ leaf.setElement((SequenceI) jvseq);
leaf.setPlaceholder(false);
}
else
*/
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);
}
else
{
- System.err.println("WARNING: Unassociated treeNode "
+ jalview.bin.Console.errPrintln("WARNING: Unassociated treeNode "
+ tnode.element().toString() + " "
+ ((tnode.getName() != null)
? " label " + tnode.getName()
occurence = Integer.valueOf(oval).intValue();
} catch (Exception e)
{
- System.err.println("Invalid nodespec '" + nodespec + "'");
+ jalview.bin.Console.errPrintln("Invalid nodespec '" + nodespec + "'");
return null;
}
jalview.datamodel.BinaryNode bn = null;
{
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;
}