/**
* Creates an object to simulate data for a given set of models, a tree, parameters and unobserved
* states. A different model can be given for each rate class.
*
* @param m Map from site class to model
* @param t The tree
* @param p The parameters
* @param unobserved The unobserved states
* @throws Models.RateCategory.RateException Thrown if there is an issue with a rate category in
* the model (e.g. a badly formatted rate).
* @throws Models.Model.ModelException Thrown if there is a problem with the model (e.g. the rate
* categories differ in their states)
* @throws TreeException Thrown if there is a problem with the tree.
* @throws Parameters.Parameters.ParameterException Thrown if there is a problem with the
* parameters (e.g. a required parameter is not present)
*/
public Simulate(Map<String, Model> m, Tree t, Parameters p, Alignment unobserved)
throws RateException, ModelException, TreeException, ParameterException {
P = new HashMap<>();
for (Entry<String, Model> e : m.entrySet()) {
P.put(e.getKey(), new Probabilities(e.getValue(), t, p));
}
this.missing = unobserved;
this.t = new HashMap<>();
for (String s : m.keySet()) {
this.t.put(s, t);
}
random = new Random();
// If the parameters setting doesn't include branch lengths parameters then
// add them from the tree. The paramter / branch length interaction is a
// bit counter-inutative and probably needs changing but in the mean time
// this is here to make errors less likely.
for (Branch b : t) {
if (!p.hasParam(b.getChild())) {
p.addParameter(Parameter.newFixedParameter(b.getChild(), b.getLength()));
}
}
}
/**
* Gets a simulated site. Recodes the simulated data before returning. For example if both "A" and
* "B" are unobserved states representing an observed state of "0" then this can be used to change
* "A" and "B" to zero. This is necessary as the simulator generates unobserved states by default.
* The returned site will have ambiguous data set as appropriate.
*
* @param recode Map of recodings
* @param internal Whether to return the state of the internal nodes
* @param siteClass The site class to simulate for
* @return The simulated site
* @throws Simulations.Simulate.SimulationException Thrown if there is a problem with the
* simulation (currently only if attempting to simulate for a site class we don't have a model
* for)
* @throws Models.RateCategory.RateException if a rate category uses the FitzJohn method at the
* root as this method requires likelihoods to calculate the frequency and we don't have the
* likelihoods when simulating.
*/
public Site getSite(boolean internal, Map<String, String> recode, String siteClass)
throws SimulationException, RateException {
if (!P.containsKey(siteClass)) {
throw new SimulationException("No model defined for requested class");
}
if (!t.containsKey(siteClass)) {
throw new SimulationException("No tree defined for requested class");
}
Site site, loSite;
do {
HashMap<String, String> assign = new HashMap<>();
RateCategory r = getRandomRate(P.get(siteClass).getRateCategory(), siteClass);
// Assign the root
assign.put(t.get(siteClass).getRoot(), getRandomStart(r, siteClass));
// Traverse the tree, assign values to nodes
for (Branch b : t.get(siteClass).getBranchesReversed()) {
assign.put(b.getChild(), getRandomChar(r, b, assign.get(b.getParent()), siteClass));
}
// Done like this so things are in a sensible order if written out
// Keeps a leaf only and all nodes copy.
LinkedHashMap<String, String> all = new LinkedHashMap<>();
LinkedHashMap<String, String> lo = new LinkedHashMap<>();
for (String l : t.get(siteClass).getLeaves()) {
all.put(l, assign.get(l));
lo.put(l, assign.get(l));
}
for (String i : t.get(siteClass).getInternal()) {
all.put(i, assign.get(i));
}
// This deals with recoding as discussed in the javadoc. If there
// is none simply ceate the site
if (recode == null) {
site = new Site(all, siteClass);
loSite = new Site(lo, siteClass);
} else {
// Else make an ambiguous data structure
Map<String, Set<String>> ambig = new HashMap<>();
// Step through the recodings and add the apropiate date to
// ambig
for (Entry<String, String> e : recode.entrySet()) {
if (!ambig.containsKey(e.getValue())) {
ambig.put(e.getValue(), new HashSet<String>());
}
ambig.get(e.getValue()).add(e.getKey());
}
// Create the sites
site = new Site(all, new Ambiguous(ambig), siteClass);
loSite = new Site(lo, new Ambiguous(ambig), siteClass);
// Now recode them
site = site.recode(recode);
loSite = loSite.recode(recode);
}
}
// While the site is missing generate another site
while (isMissing(loSite));
if (internal) {
return site;
} else {
return loSite;
}
}