/**
* name suitable for printing - quotes if necessary
*
* @param taxon
* @param builder
* @return
*/
private StringBuilder appendTaxonName(Taxon taxon, StringBuilder builder) {
String name = taxon.getId();
if (!name.matches(SPECIAL_CHARACTERS_REGEX)) {
// JEBL way of quoting the quote character
name = name.replace("\'", "\'\'");
builder.append("\'").append(name).append("\'");
return builder;
}
return builder.append(name);
}
public String asText(int indentlen) {
StringBuilder s = new StringBuilder();
Formatter formatter = new Formatter(s, Locale.US);
if (lft < 0) {
formatter.format("%s ", taxon.getId());
} else {
formatter.format("%s ", "+");
}
while (s.length() < 20 - indentlen) {
formatter.format("%s", " ");
}
formatter.format("%s ", AlloppMisc.nonnegIn8Chars(height));
formatter.format("%20s ", AlloppMisc.FixedBitSetasText(union));
formatter.format("%3d ", nlineages);
for (int c = 0; c < coalheights.size(); c++) {
formatter.format(AlloppMisc.nonnegIn8Chars(coalheights.get(c)) + ",");
}
return s.toString();
}
public static void main(String[] arg) throws IOException {
// READ DEMOGRAPHIC FUNCTION
String filename = arg[0];
BufferedReader reader = new BufferedReader(new FileReader(filename));
double popSizeScale = 1.0;
double generationTime = 1.0;
if (arg.length > 2) {
popSizeScale = Double.parseDouble(arg[2]);
}
if (arg.length > 3) {
generationTime = Double.parseDouble(arg[3]);
}
PrintWriter populationFuncLogger = null;
if (arg.length > 5) {
String logFileName = arg[5];
if (logFileName.equals("-")) {
populationFuncLogger = new PrintWriter(System.out);
} else {
populationFuncLogger = new PrintWriter(new FileWriter(logFileName));
}
}
List<Double> times = new ArrayList<Double>();
String line = reader.readLine();
String[] tokens = line.trim().split("[\t ]+");
if (tokens.length < 2) throw new RuntimeException();
ArrayList<ArrayList> popSizes = new ArrayList<ArrayList>();
while (line != null) {
double time = Double.parseDouble(tokens[0]) / generationTime;
times.add(time);
for (int i = 1; i < tokens.length; i++) {
popSizes.add(new ArrayList<Double>());
popSizes.get(i - 1).add(Double.parseDouble(tokens[i]));
}
line = reader.readLine();
if (line != null) {
tokens = line.trim().split("[\t ]+");
if (tokens.length != popSizes.size() + 1) throw new RuntimeException();
}
}
reader.close();
// READ SAMPLE TIMES
String samplesFilename = arg[1];
reader = new BufferedReader(new FileReader(samplesFilename));
line = reader.readLine();
Taxa taxa = new Taxa();
int id = 0;
while (line != null) {
if (!line.startsWith("#")) {
tokens = line.split("[\t ]+");
if (tokens.length == 4) {
double t0 = Double.parseDouble(tokens[0]);
double t1 = Double.parseDouble(tokens[1]);
double dt = Double.parseDouble(tokens[2]);
int k = Integer.parseInt(tokens[3]);
for (double time = t0; time <= t1; time += dt) {
double sampleTime = time / generationTime;
for (int i = 0; i < k; i++) {
Taxon taxon = new Taxon("t" + id);
taxon.setAttribute(
dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
taxa.addTaxon(taxon);
id += 1;
}
}
} else {
// sample times are in the same units as simulation
double sampleTime = Double.parseDouble(tokens[0]) / generationTime;
int count = Integer.parseInt(tokens[1]);
for (int i = 0; i < count; i++) {
Taxon taxon = new Taxon(id + "");
taxon.setAttribute(
dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
taxa.addTaxon(taxon);
id += 1;
}
}
}
line = reader.readLine();
}
double minTheta = Double.MAX_VALUE;
double maxTheta = 0.0;
PrintWriter out;
if (arg.length > 4) {
out = new PrintWriter(new FileWriter(arg[4]));
} else {
out = new PrintWriter(System.out);
}
int pp = 0;
for (List<Double> popSize : popSizes) {
double[] thetas = new double[popSize.size()];
double[] intervals = new double[times.size() - 1];
if (populationFuncLogger != null) {
populationFuncLogger.println("# " + pp);
++pp;
}
// must reverse the direction of the model
for (int j = intervals.length; j > 0; j--) {
intervals[intervals.length - j] = times.get(j) - times.get(j - 1);
final double theta = popSize.get(j) * popSizeScale;
thetas[intervals.length - j] = theta;
if (theta < minTheta) {
minTheta = theta;
}
if (theta > maxTheta) {
maxTheta = theta;
}
final double t = times.get(intervals.length) - times.get(j);
if (populationFuncLogger != null) {
populationFuncLogger.println(t + "\t" + theta);
}
}
if (debug != null) {
debug.println("min theta = " + minTheta);
debug.println("max theta = " + maxTheta);
}
PiecewiseLinearPopulation demo =
new PiecewiseLinearPopulation(intervals, thetas, Units.Type.GENERATIONS);
CoalescentSimulator simulator = new CoalescentSimulator();
Tree tree = simulator.simulateTree(taxa, demo);
out.println(Tree.Utils.newick(tree));
if (debug != null) {
debug.println(Tree.Utils.newick(tree));
}
}
if (populationFuncLogger != null) {
populationFuncLogger.flush();
populationFuncLogger.close();
}
out.flush();
out.close();
}