@Override
public void makeDirty() {
super.makeDirty();
updateSiteModel = true;
updateSubstitutionModel = true;
updateRestrictedNodePartials = true;
}
/** Stores the additional state other than model components */
protected void storeState() {
partialBufferHelper.storeState();
substitutionModelDelegate.storeState();
if (useScaleFactors || useAutoScaling) { // Only store when actually used
scaleBufferHelper.storeState();
System.arraycopy(
scaleBufferIndices, 0, storedScaleBufferIndices, 0, scaleBufferIndices.length);
// storedRescalingCount = rescalingCount;
}
super.storeState();
}
/** Restore the additional stored state */
protected void restoreState() {
updateSiteModel =
true; // this is required to upload the categoryRates to BEAGLE after the restore
partialBufferHelper.restoreState();
substitutionModelDelegate.restoreState();
if (useScaleFactors || useAutoScaling) {
scaleBufferHelper.restoreState();
int[] tmp = storedScaleBufferIndices;
storedScaleBufferIndices = scaleBufferIndices;
scaleBufferIndices = tmp;
// rescalingCount = storedRescalingCount;
}
updateRestrictedNodePartials = true;
super.restoreState();
}
/** Handles model changed events from the submodels. */
protected void handleModelChangedEvent(Model model, Object object, int index) {
fireModelChanged();
if (model == treeModel) {
if (object instanceof TreeModel.TreeChangedEvent) {
if (((TreeModel.TreeChangedEvent) object).isNodeChanged()) {
// If a node event occurs the node and its two child nodes
// are flagged for updating (this will result in everything
// above being updated as well. Node events occur when a node
// is added to a branch, removed from a branch or its height or
// rate changes.
updateNodeAndChildren(((TreeModel.TreeChangedEvent) object).getNode());
updateRestrictedNodePartials = true;
} else if (((TreeModel.TreeChangedEvent) object).isTreeChanged()) {
// Full tree events result in a complete updating of the tree likelihood
// This event type is now used for EmpiricalTreeDistributions.
// System.err.println("Full tree update event - these events currently
// aren't used\n" +
// "so either this is in error or a new feature is using them
// so remove this message.");
updateAllNodes();
updateRestrictedNodePartials = true;
} else {
// Other event types are ignored (probably trait changes).
// System.err.println("Another tree event has occured (possibly a trait change).");
}
}
} else if (model == branchRateModel) {
if (index == -1) {
if (COUNT_TOTAL_OPERATIONS) totalRateUpdateAllCount++;
updateAllNodes();
} else {
if (COUNT_TOTAL_OPERATIONS) totalRateUpdateSingleCount++;
updateNode(treeModel.getNode(index));
}
} else if (model == branchModel) {
// if (index == -1) {
// updateSubstitutionModel = true;
// updateAllNodes();
// } else {
// updateNode(treeModel.getNode(index));
// }
makeDirty();
} else if (model == siteModel) {
updateSiteModel = true;
updateAllNodes();
} else if (model == tipStatesModel) {
if (object instanceof Taxon) {
for (int i = 0; i < treeModel.getNodeCount(); i++)
if (treeModel.getNodeTaxon(treeModel.getNode(i)) != null
&& treeModel
.getNodeTaxon(treeModel.getNode(i))
.getId()
.equalsIgnoreCase(((Taxon) object).getId())) updateNode(treeModel.getNode(i));
} else updateAllNodes();
} else {
throw new RuntimeException("Unknown componentChangedEvent");
}
super.handleModelChangedEvent(model, object, index);
}