exit(1);
}
}
+//**********************************************************************************************************************
+string MetaStatsCommand::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 == "metastats") { outputFileName = "metastats"; }
+ 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, "MetaStatsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(){
try {
string setB = namesOfGroupCombos[c][1];
//get filename
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + "." + getOutputFileNameTag("metastats");
outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
//int nameLength = outputFileName.length();
//char * output = new char[nameLength];
outputNames.pop_back();
}else {
- ofstream outTemp;
- string tempOut = outputDir + "data." + setA + "-" + setB + ".matrix";
- m->openOutputFile(tempOut, outTemp);
- for (int i = 0; i < subset.size(); i++) { outTemp << '\t' << subset[i]->getGroup(); }
- outTemp << endl;
-
-
//fill data
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
//data[j] = new double[subset.size()];
data2[j].resize(subset.size(), 0.0);
- outTemp << "OTU" << (j+1);
+
for (int i = 0; i < subset.size(); i++) {
data2[j][i] = (subset[i]->getAbundance(j));
- outTemp << '\t' << subset[i]->getAbundance(j);
}
- outTemp << endl;
}
- outTemp.close();
+
m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine();
//metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);