private void parseHeader(String lineHeader) {
String header = lineHeader.substring(1, lineHeader.length());
String[] allFields = header.split("\t");
allFields = Arrays.copyOfRange(allFields, 6, allFields.length);
for (int i = 0; i < allFields.length; i++) {
ped.getFields().put(allFields[i], i);
}
}
@Override
public List<Pedigree> read() {
String line;
Individual ind, father, mother;
String[] fields;
String sampleId, familyId, fatherId, motherId, sex, phenotype;
Set<Individual> family;
String[] auxFields = null;
try {
while ((line = reader.readLine()) != null) {
if (line.startsWith("#")) {
this.parseHeader(line);
} else {
fields = line.split("\t", -1);
familyId = fields[0];
sampleId = fields[1];
fatherId = fields[2];
motherId = fields[3];
sex = fields[4];
phenotype = fields[5];
if (fields.length > 6) {
auxFields = Arrays.copyOfRange(fields, 6, fields.length);
}
family = ped.getFamily(familyId);
if (family == null) {
family = new TreeSet<>();
ped.addFamily(familyId, family);
}
ind = new Individual(sampleId, familyId, null, null, sex, phenotype, auxFields);
ind.setFatherId(fatherId);
ind.setMotherId(motherId);
ped.addIndividual(ind);
family.add(ind);
}
}
} catch (IOException e) {
e.printStackTrace();
}
for (Map.Entry<String, Individual> entry : ped.getIndividuals().entrySet()) {
ind = entry.getValue();
father = ped.getIndividual(ind.getFatherId());
mother = ped.getIndividual(ind.getMotherId());
ind.setFather(father);
ind.setMother(mother);
if (mother != null) {
mother.addChild(ind);
}
if (father != null) {
father.addChild(ind);
}
}
return Arrays.asList(ped);
}