/**
* The list is in ascending (time) order, i.e., patient matrix would come before follow-up
* matrices.
*/
@Override
public SurvivalStatus computeSurvivalData(List<DataMatrix> dataMatrices) {
canonicalPatientList = getPatientIds(dataMatrices.get(0));
SurvivalStatus oss = new SurvivalStatus();
computeSurvivalData(oss, getSurvivalData(dataMatrices));
computeDiseaseFreeData(oss, getDiseaseFreeData(dataMatrices));
return oss;
}
private Map<String, DiseaseFreeData> getDiseaseFreeDataForMatrix(DataMatrix dataMatrix) {
Map<String, DiseaseFreeData> diseaseFreeDataMap = new HashMap<String, DiseaseFreeData>();
List<String> patientIds = getPatientIds(dataMatrix);
for (int lc = 0; lc < patientIds.size(); lc++) {
String patientId = patientIds.get(lc);
DiseaseFreeData df = getDiseaseFreeDataForPatient(lc, dataMatrix);
if (diseaseFreeDataMap.containsKey(patientId)) {
df = mergeDiseaseFreeData(diseaseFreeDataMap.get(patientId), df);
}
diseaseFreeDataMap.put(patientId, df);
}
return diseaseFreeDataMap;
}
private Map<String, SurvivalData> getSurvivalDataForMatrix(DataMatrix dataMatrix) {
Map<String, SurvivalData> survivalDataMap = new HashMap<String, SurvivalData>();
List<String> patientIds = getPatientIds(dataMatrix);
for (int lc = 0; lc < patientIds.size(); lc++) {
String patientId = patientIds.get(lc);
SurvivalData sd = getSurvivalDataForPatient(lc, dataMatrix);
if (survivalDataMap.containsKey(patientId)) {
sd = mergeSurvivalData(survivalDataMap.get(patientId), sd);
}
survivalDataMap.put(patientId, sd);
}
return survivalDataMap;
}