/**
* Simulates a coalescent tree from a set of subtrees.
*
* @param subtrees an array of tree to be used as subtrees
* @param model the demographic model to use
* @param rootHeight an optional root height with which to scale the whole tree
* @param preserveSubtrees true of subtrees should be preserved
* @return a simulated coalescent tree
*/
public SimpleTree simulateTree(
Tree[] subtrees, DemographicModel model, double rootHeight, boolean preserveSubtrees) {
SimpleNode[] roots = new SimpleNode[subtrees.length];
SimpleTree tree;
for (int i = 0; i < roots.length; i++) {
roots[i] = new SimpleNode(subtrees[i], subtrees[i].getRoot());
}
// if just one taxonList then finished
if (roots.length == 1) {
tree = new SimpleTree(roots[0]);
} else {
tree = new SimpleTree(simulator.simulateCoalescent(roots, model.getDemographicFunction()));
}
if (!Double.isNaN(rootHeight) && rootHeight > 0.0) {
if (preserveSubtrees) {
limitNodes(tree, rootHeight - 1e-12);
tree.setRootHeight(rootHeight);
} else {
attemptToScaleTree(tree, rootHeight);
}
}
return tree;
}
private void remove() {
final SimpleNode[] nodes = myTree.getSelectedNodesIfUniform();
for (final SimpleNode node : nodes) {
if (node instanceof FileSetNode) {
final OfbizFileSet fileSet = ((FileSetNode) node).mySet;
if (fileSet.getFiles().isEmpty()) {
myBuffer.remove(fileSet);
return;
}
final int result =
Messages.showYesNoDialog(
myPanel,
String.format("Remove File Set '%s' ?", fileSet.getName()),
"Confirm removal",
Messages.getQuestionIcon());
if (result == DialogWrapper.OK_EXIT_CODE) {
if (fileSet.isAutodetected()) {
fileSet.setRemoved(true);
myBuffer.add(fileSet);
} else {
myBuffer.remove(fileSet);
}
}
} else if (node instanceof ConfigFileNode) {
final VirtualFilePointer filePointer = ((ConfigFileNode) node).myFilePointer;
final OfbizFileSet fileSet = ((FileSetNode) node.getParent()).mySet;
fileSet.removeFile(filePointer);
}
}
}
private void selectFileSet(final OfbizFileSet fileSet) {
myTree.select(
myBuilder,
new SimpleNodeVisitor() {
public boolean accept(final SimpleNode simpleNode) {
if (simpleNode instanceof FileSetNode) {
if (((FileSetNode) simpleNode).mySet.equals(fileSet)) {
return true;
}
}
return false;
}
},
false);
}
@Nullable
private FileSetNode getCurrentFileSetNode() {
final SimpleNode selectedNode = myTree.getSelectedNode();
if (selectedNode == null) {
return null;
}
if (selectedNode instanceof FileSetNode) {
return (FileSetNode) selectedNode;
} else if (selectedNode.getParent() instanceof FileSetNode) {
return (FileSetNode) selectedNode.getParent();
} else {
final SimpleNode parent = selectedNode.getParent();
if (parent != null && parent.getParent() instanceof FileSetNode) {
return (FileSetNode) selectedNode.getParent().getParent();
}
}
return null;
}
@Override
public int getTaxonCount() {
return stree.getTaxonCount();
}
@Override
public boolean hasBranchLengths() {
return stree.hasBranchLengths();
}
@Override
public Iterator<String> getAttributeNames() {
return stree.getAttributeNames();
}
@Override
public Iterator<Taxon> iterator() {
return stree.iterator();
}
@Override
public void setUnits(Type units) {
stree.setUnits(units);
}
@Override
public int getTaxonIndex(String id) {
return stree.getTaxonIndex(id);
}
@Override
public List<Taxon> asList() {
return stree.asList();
}
@Override
public boolean isRoot(NodeRef node) {
return stree.isRoot(node);
}
@Override
public int getChildCount(NodeRef node) {
return stree.getChildCount(node);
}
@Override
public Iterator getNodeAttributeNames(NodeRef node) {
return stree.getNodeAttributeNames(node);
}
@Override
public boolean isExternal(NodeRef node) {
return stree.isExternal(node);
}
@Override
public Object getNodeAttribute(NodeRef node, String name) {
return stree.getNodeAttribute(node, name);
}
@Override
public double getNodeRate(NodeRef node) {
return stree.getNodeRate(node);
}
@Override
public double getBranchLength(NodeRef node) {
return stree.getBranchLength(node);
}
@Override
public Taxon getTaxon(int taxonIndex) {
return stree.getTaxon(taxonIndex);
}
@Override
public NodeRef getChild(NodeRef node, int j) {
return stree.getChild(node, j);
}
@Override
public String getTaxonId(int taxonIndex) {
return stree.getTaxonId(taxonIndex);
}
@Override
public NodeRef getParent(NodeRef node) {
return stree.getParent(node);
}
@Override
public int getTaxonIndex(Taxon taxon) {
return stree.getTaxonIndex(taxon);
}
@Override
public boolean hasNodeHeights() {
return stree.hasNodeHeights();
}
@Override
public Object getTaxonAttribute(int taxonIndex, String name) {
return stree.getTaxonAttribute(taxonIndex, name);
}
@Override
public void setAttribute(String name, Object value) {
stree.setAttribute(name, value);
}
@Override
public Type getUnits() {
return stree.getUnits();
}
@Override
public Object getAttribute(String name) {
return stree.getAttribute(name);
}
@Override
public Tree getCopy() {
return stree.getCopy();
}
@Override
public double getNodeHeight(NodeRef node) {
return stree.getNodeHeight(node);
}
