globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
- util = new SharedUtil();
-
+
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
TreeGroupCommand::~TreeGroupCommand(){
delete input;
delete read;
- delete util;
}
//**********************************************************************************************************************
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; }
+ if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
numGroups = globaldata->Groups.size();
groupNames = "";
//create a new filename
outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
-
+
+
for (int k = 0; k < lookup.size(); k++) {
for (int l = k; l < lookup.size(); l++) {
if (k != l) { //we dont need to similiarity of a groups to itself
createTree();
}
}
-
+
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
//get next line to process
lookup = input->getSharedRAbundVectors();
count++;
}
}
/***********************************************************/
-void TreeGroupCommand::printSims() {
+void TreeGroupCommand::printSims(ostream& out) {
try {
- cout << "simsMatrix" << endl;
+
+ //output column headers
+ out << '\t';
+ for (int i = 0; i < lookup.size(); i++) { out << lookup[i]->getGroup() << '\t'; }
+ out << endl;
+
+
for (int m = 0; m < simMatrix.size(); m++) {
+ out << lookup[m]->getGroup() << '\t';
for (int n = 0; n < simMatrix.size(); n++) {
- cout << simMatrix[m][n] << '\t';
+ out << simMatrix[m][n] << '\t';
}
- cout << endl;
+ out << endl;
}
}