public String solvePedigree() {
renumberAll();
updateDisplay();
String integrity = checkIntegrity(history.lastElement());
if (integrity.equals("")) {
StringBuffer b = new StringBuffer();
PedigreeSolver ps = new PedigreeSolver(getAllPeople(), getMatingList());
PedigreeSolution sol = ps.solve();
PedigreeSolution consolidatedSol = ps.consolidate(sol);
b.append(consolidatedSol + "\n");
return b.toString();
} else {
return integrity;
}
}
public String getGrade() {
Document d = XMLParser.createDocument();
Element root = d.createElement("Grade");
// first, some specifications of the pedigree
int numMales = 0;
int numFemales = 0;
int numAffectedMales = 0;
int numAffectedFemales = 0;
PelicanPerson[] people = getAllPeople();
for (int i = 0; i < people.length; i++) {
PelicanPerson p = people[i];
if (p.sex == PelicanPerson.male) {
numMales++;
if (p.affection == PelicanPerson.affected) {
numAffectedMales++;
}
} else {
numFemales++;
if (p.affection == PelicanPerson.affected) {
numAffectedFemales++;
}
}
}
Element e = d.createElement("Counts");
Element M = d.createElement("M");
M.appendChild(d.createTextNode(String.valueOf(numMales)));
e.appendChild(M);
Element F = d.createElement("F");
F.appendChild(d.createTextNode(String.valueOf(numFemales)));
e.appendChild(F);
Element aM = d.createElement("aM");
aM.appendChild(d.createTextNode(String.valueOf(numAffectedMales)));
e.appendChild(aM);
Element aF = d.createElement("aF");
aF.appendChild(d.createTextNode(String.valueOf(numAffectedFemales)));
e.appendChild(aF);
root.appendChild(e);
// now, the analysis results
renumberAll();
updateDisplay();
String integrity = checkIntegrity(history.lastElement());
if (integrity.equals("")) {
PedigreeSolver ps = new PedigreeSolver(getAllPeople(), getMatingList());
PedigreeSolution sol = ps.solve();
e = d.createElement("Analysis");
GenotypeSet[] results = sol.getResults();
Element AR = d.createElement("AR");
if (results[0].getAll().size() > 0) {
AR.appendChild(d.createTextNode("Y"));
} else {
AR.appendChild(d.createTextNode("N"));
}
e.appendChild(AR);
Element AD = d.createElement("AD");
if (results[1].getAll().size() > 0) {
AD.appendChild(d.createTextNode("Y"));
} else {
AD.appendChild(d.createTextNode("N"));
}
e.appendChild(AD);
Element SR = d.createElement("SR");
if (results[2].getAll().size() > 0) {
SR.appendChild(d.createTextNode("Y"));
} else {
SR.appendChild(d.createTextNode("N"));
}
e.appendChild(SR);
Element SD = d.createElement("SD");
if (results[3].getAll().size() > 0) {
SD.appendChild(d.createTextNode("Y"));
} else {
SD.appendChild(d.createTextNode("N"));
}
e.appendChild(SD);
}
root.appendChild(e);
return root.toString();
}
