}
}
//**********************************************************************************************************************
+string MatrixOutputCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "phylip") { outputFileName = "dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){
try {
abort = true; calledHelp = true;
else { subsample = false; }
}
- if (subsample == false) { iters = 1; }
+ if (subsample == false) { iters = 0; }
if (abort == false) {
out << endl;
}
}else{
- for (int b = 0; b < simMatrix.size(); m++) {
+ for (int b = 0; b < simMatrix.size(); b++) {
out << lookup[b]->getGroup() << '\t';
for (int n = 0; n < simMatrix[b].size(); n++) {
out << simMatrix[b][n] << '\t';
matrix[column][row] = dist;
}
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + "." + getOutputFileNameTag("phylip");
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+
ofstream outDist;
m->openOutputFile(distFileName, outDist);
outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
}
- if (iters != 1) {
+ if (iters != 0) {
//we need to find the average distance and standard deviation for each groups distance
vector< vector<seqDist> > calcAverages; calcAverages.resize(matrixCalculators.size());
stdmatrix[column][row] = stdDist;
}
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".ave.dist";
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".ave." + getOutputFileNameTag("phylip");
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outAve;
m->openOutputFile(distFileName, outAve);
outAve.close();
- distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".std.dist";
+ distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".std." + getOutputFileNameTag("phylip");
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outSTD;
m->openOutputFile(distFileName, outSTD);