private List<String> initializeList(int size) {
List<String> os = new ArrayList<String>(size);
for (int lc = 0; lc < size; lc++) {
os.add(lc, "");
}
return os;
}
private List<String> convertFollowupPatientIds(List<String> patientIds) {
List<String> convertedPatientIds = new ArrayList<String>();
for (String patientId : patientIds) {
Matcher patientIdMatcher = FOLLOW_UP_PATIENT_ID_REGEX.matcher(patientId);
convertedPatientIds.add(patientIdMatcher.find() ? patientIdMatcher.group(1) : patientId);
}
return convertedPatientIds;
}
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;
}
/**
* 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 void printList(List<String> list) {
System.out.print("(");
int ct = 0;
for (String value : list) {
if (value.isEmpty()) {
value = "[]";
}
System.out.print(value);
if (++ct < list.size()) {
System.out.print(", ");
}
}
System.out.print(")\t\t");
}
private List<String> computeOverallSurvivalStatus(Map<String, SurvivalData> survivalData) {
List<String> osStatus = initializeList(canonicalPatientList.size());
for (String patientId : survivalData.keySet()) {
int osStatusIndex = canonicalPatientList.indexOf(patientId);
SurvivalData sd = survivalData.get(patientId);
if (VitalStatusAlive.has(sd.vitalStatus)) {
osStatus.set(osStatusIndex, VitalStatusAlive.LIVING.toString());
} else if (VitalStatusDead.has(sd.vitalStatus)) {
osStatus.set(osStatusIndex, VitalStatusDead.DECEASED.toString());
} else {
osStatus.set(osStatusIndex, ClinicalAttribute.NA);
}
}
return osStatus;
}
private List<String> computeOverallSurvivalMonths(Map<String, SurvivalData> survivalData) {
List<String> osStatusMonths = initializeList(canonicalPatientList.size());
for (String patientId : survivalData.keySet()) {
int osStatusMonthsIndex = canonicalPatientList.indexOf(patientId);
SurvivalData sd = survivalData.get(patientId);
if (VitalStatusAlive.has(sd.vitalStatus)) {
osStatusMonths.set(
osStatusMonthsIndex, convertDaysToMonths(sd.lastFollowUp, sd.lastKnownAlive));
} else if (VitalStatusDead.has(sd.vitalStatus)) {
osStatusMonths.set(osStatusMonthsIndex, convertDaysToMonths(sd.daysToDeath));
} else {
osStatusMonths.set(osStatusMonthsIndex, ClinicalAttribute.NA);
}
}
return osStatusMonths;
}
private List<String> computeDiseaseFreeStatus(Map<String, DiseaseFreeData> diseaseFreeData) {
List<String> dfStatus = initializeList(canonicalPatientList.size());
for (String patientId : diseaseFreeData.keySet()) {
int dfStatusIndex = canonicalPatientList.indexOf(patientId);
DiseaseFreeData df = diseaseFreeData.get(patientId);
if (patientIsDiseaseFree(df)) {
dfStatus.set(dfStatusIndex, DiseaseFreeStatus.DISEASE_FREE.toString());
} else {
try {
Integer.parseInt(df.daysToNewTumorEventAfterInitialTreatment);
dfStatus.set(dfStatusIndex, DiseaseFreeStatus.DISEASED.toString());
} catch (NumberFormatException e) {
dfStatus.set(dfStatusIndex, ClinicalAttribute.NA);
}
}
}
return dfStatus;
}
private List<String> computeDiseaseFreeMonths(Map<String, DiseaseFreeData> diseaseFreeData) {
List<String> dfStatusMonths = initializeList(canonicalPatientList.size());
for (String patientId : diseaseFreeData.keySet()) {
int dfStatusMonthsIndex = canonicalPatientList.indexOf(patientId);
DiseaseFreeData df = diseaseFreeData.get(patientId);
try {
if (patientIsDiseaseFree(df)) {
dfStatusMonths.set(
dfStatusMonthsIndex, convertDaysToMonths(df.lastFollowUp, df.lastKnownAlive));
} else {
int dfStatusDays = Integer.parseInt(df.daysToNewTumorEventAfterInitialTreatment);
dfStatusMonths.set(
dfStatusMonthsIndex, convertDaysToMonths(Integer.toString(dfStatusDays)));
}
} catch (NumberFormatException e) {
dfStatusMonths.set(dfStatusMonthsIndex, ClinicalAttribute.NA);
}
}
return dfStatusMonths;
}
private void dumpSurvivalData(Map<String, List<SurvivalData>> survivalData) {
List<String> daysToDeath = new ArrayList<String>();
List<String> lastFollowUp = new ArrayList<String>();
List<String> lastKnownAlive = new ArrayList<String>();
List<String> vitalStatus = new ArrayList<String>();
for (String patientId : new TreeSet<String>(survivalData.keySet())) {
for (SurvivalData sd : survivalData.get(patientId)) {
daysToDeath.add(sd.daysToDeath);
lastFollowUp.add(sd.lastFollowUp);
lastKnownAlive.add(sd.lastKnownAlive);
vitalStatus.add(sd.vitalStatus);
}
System.out.print(patientId + "\t\t");
printList(daysToDeath);
printList(lastFollowUp);
printList(lastKnownAlive);
printList(vitalStatus);
System.out.println();
daysToDeath.clear();
lastFollowUp.clear();
lastKnownAlive.clear();
vitalStatus.clear();
}
}