@SuppressWarnings("unchecked")
public void sync(int iPartition) {
if (parentInputs.size() > 0 && _input.get() != null) {
Input<?> input = parentInputs.get(iPartition);
if (bIsList) {
List<Object> list = (List<Object>) _input.get();
List<Object> targetList = ((List<Object>) input.get());
// targetList.clear();
// only clear former members
for (BEASTInterface plugin : startInputs) {
targetList.remove(plugin);
}
targetList.addAll(list);
// sync outputs of items in list
for (Object o : list) {
if (o instanceof BEASTInterface) {
((BEASTInterface) o).getOutputs().add(parentPlugins.get(iPartition));
}
}
} else {
try {
// System.err.println("sync " + parentPlugins.get(iPartition) + "[" + input.getName() + "]
// = " + _input.get());
input.setValue(_input.get(), parentPlugins.get(iPartition));
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
/**
* @param newick a string representing a tree in newick format
* @param adjustTipHeights true if the tip heights should be adjusted to 0 (i.e. contemporaneous)
* after reading in tree.
* @param allowSingleChildNodes true if internal nodes with single children are allowed
* @param isLabeled true if nodes are labeled with taxa labels
* @param offset if isLabeled == false and node labeling starts with x then offset should be x.
* When isLabeled == true offset should be 1 as by default.
* @throws Exception
*/
public TreeParser(
final String newick,
final boolean adjustTipHeights,
final boolean allowSingleChildNodes,
final boolean isLabeled,
final int offset)
throws Exception {
newickInput.setValue(newick, this);
isLabelledNewickInput.setValue(isLabeled, this);
adjustTipHeightsInput.setValue(adjustTipHeights, this);
allowSingleChildInput.setValue(allowSingleChildNodes, this);
offsetInput.setValue(offset, this);
initAndValidate();
}
/**
* Create a tree from the given newick format
*
* @param taxaNames a list of taxa names to use, or null. If null then IsLabelledNewick will be
* set to true
* @param newick the newick of the tree
* @param offset the offset to map node numbers in newick format to indices in taxaNames. so,
* name(node with nodeNumber) = taxaNames[nodeNumber-offset]
* @param adjustTipHeightsWhenMissingDateTraits true if tip heights should be adjusted to zero
* @throws Exception
*/
public TreeParser(
final List<String> taxaNames,
final String newick,
final int offset,
final boolean adjustTipHeightsWhenMissingDateTraits)
throws Exception {
if (taxaNames == null) {
isLabelledNewickInput.setValue(true, this);
} else {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(taxaNames)), this);
}
newickInput.setValue(newick, this);
offsetInput.setValue(offset, this);
adjustTipHeightsInput.setValue(adjustTipHeightsWhenMissingDateTraits, this);
labels = taxaNames;
initAndValidate();
}
public TreeParser(final Alignment alignment, final String newick) throws Exception {
dataInput.setValue(alignment, this);
newickInput.setValue(newick, this);
initAndValidate();
}