public List<Family> getFamiliesTDT() {
List<Family> families = new ArrayList<>();
Individual ind;
for (Map.Entry<String, Individual> entry : this.individuals.entrySet()) {
ind = entry.getValue();
if (ind.getFather() != null && ind.getMother() != null) {
addIndividualToFamily(ind, ind.getFather(), ind.getMother(), families);
}
}
return families;
}
public boolean needsToRun(Run run, int generation) {
Population pop = getPopulationFor(run, generation);
int count = run.getIntProperty(GenetikConstants.POPULATION, Integer.MAX_VALUE, true);
int scoreCount = 0;
for (int i = 0, max = pop.size(); i < max; i++) {
Individual ind = pop.get(i);
if (ind.hasFitness() && ind.hasScores()) {
scoreCount++;
}
}
return scoreCount != count;
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Pedigree\n");
if (fields.size() > 0) {
sb.append("fields = " + fields.keySet().toString() + "\n");
}
for (Map.Entry<String, Set<Individual>> elem : this.families.entrySet()) {
sb.append(elem.getKey() + "\n");
for (Individual ind : elem.getValue()) {
sb.append("\t" + ind.toString() + "\n");
}
}
return sb.toString();
}
/** Saves an individual to disk under a given filename, in computer-readable format. */
public void storeIndividual(final EvolutionState state, String filename, Individual ind) {
try {
File file = openFile(state, filename);
// PrintWriter writer = new PrintWriter(file);
// ind.printIndividual(state, writer);
// writer.close();
int log =
state.output.addLog(
file,
Output.V_NO_GENERAL - 1,
false,
!state.parameters.getBoolean(new Parameter(P_COMPRESS), null, false),
state.parameters.getBoolean(new Parameter(P_COMPRESS), null, false));
ind.printIndividual(state, log, Output.V_NO_GENERAL);
state.output.message("Best Individual stored in " + filename);
} catch (Exception e) {
state.output.error("Exception " + e);
}
}
public void addIndividual(Individual ind) {
this.individuals.put(ind.getId(), ind);
}