int ConfigClass::readConfig() {
Properties prop(configFile);
//getting driver
std::string tmp = prop.getValue("DRIVER_TYPE");
if (!tmp.empty()) {
driverType = (E_DRIVER_TYPE) getDriverType(tmp);
}
//screen width
tmp = prop.getValue("SCREEN_WIDTH");
if (!tmp.empty()) {
screenWidth = atoi(tmp.c_str());
}
//screen height
tmp = prop.getValue("SCREEN_HEIGHT");
if (!tmp.empty()) {
screenHeight = atoi(tmp.c_str());
}
//full screen
tmp = prop.getValue("FULLSCREEN");
if (!tmp.empty()) {
fullscreen = getBool(tmp);
}
//stencil
tmp = prop.getValue("STENCIL_BUFFER");
if (!tmp.empty()) {
stencil = getBool(tmp);
}
//vsync
tmp = prop.getValue("VSYNC");
if (!tmp.empty()) {
vsync = getBool(tmp);
}
//bits
tmp = prop.getValue("BITS");
if (!tmp.empty()) {
bits = atoi(tmp.c_str());
}
return 0;
}
void printSampleDriverList(vector<vector<Driver> >* driversOfAllSamples,
string pathname, vector<string>* geneIdToSymbol,
vector<string>* sampleIdToName,
TIntegerMatrix* originaloriginalPointMutationsMatrix,
TIntegerMatrix* originalCNVsMatrix, vector<int>* genesPointMut,
vector<int>* genesCNV, vector<double>* driverAggregatedScores,
vector<int>* driversFrequency, vector<int>* mutationFrequency, vector<bool>* isCancerBenchmarkGenes) {
int totalSamples = driversOfAllSamples->size();
for (int i = 0; i < totalSamples; ++i) {
vector<Driver> drivers = driversOfAllSamples->at(i);
int numDrivers = drivers.size();
list<SampleDriver> sampleDriversList;
//for each driver
for (int j = 0; j < numDrivers; ++j) {
SampleDriver driver;
driver.gene = geneIdToSymbol->at(drivers[j].geneId);
driver.type = getDriverType(drivers[j].geneId, i,
originaloriginalPointMutationsMatrix, originalCNVsMatrix,
genesPointMut, genesCNV);
driver.impactScore = drivers[j].impactScore;
driver.aggregatedImpactScore = driverAggregatedScores->at(
drivers[j].geneId);
driver.driverFrequency = 1.0
* driversFrequency->at(drivers[j].geneId) / totalSamples;
driver.mutationFrequency = 1.0
* mutationFrequency->at(drivers[j].geneId) / totalSamples;
if(isCancerBenchmarkGenes->at(drivers[j].geneId)){
driver.cancerCensus = "Y";
}else{
driver.cancerCensus = "N";
}
driver.panCancer = "NA";
sampleDriversList.push_back(driver);
}
string filename = pathname + sampleIdToName->at(i) + ".tsv";
vector<string> outputStr;
outputStr.push_back(
"GENE\tTYPE\tSAMPLE_IMPACT\tDATA_SET_IMPACT\tDRIVER_FREQUENCY\tMUTATION_FREQUENCY\tCANCER_CENSUS\tPAN_CANCER");
sampleDriversList.sort(sortByImpactScore);
for (list<SampleDriver>::iterator it = sampleDriversList.begin();
it != sampleDriversList.end(); it++) {
string str = it->gene + "\t" + it->type + "\t"
+ doubleToStr(it->impactScore, 3) + "\t"
+ doubleToStr(it->aggregatedImpactScore, 3) + "\t"
+ doubleToStr(it->driverFrequency, 3) + "\t"
+ doubleToStr(it->mutationFrequency, 3) + "\t"
+ it->cancerCensus + "\t" + it->panCancer;
outputStr.push_back(str);
}
writeStrVector(filename.c_str(), &outputStr);
}
}
