*/
#include "metastatscommand.h"
-#include "metastats.h"
#include "sharedutilities.h"
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];
m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();
outputNames.pop_back();
}else {
+
//fill data
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
//data[j] = new double[subset.size()];
data2[j].resize(subset.size(), 0.0);
+
for (int i = 0; i < subset.size(); i++) {
- //data[j][i] = (subset[i]->getAbundance(j));
data2[j][i] = (subset[i]->getAbundance(j));
}
}
MothurMetastats mothurMeta(threshold, iters);
mothurMeta.runMetastats(outputFileName , data2, setACount);
m->mothurOutEndLine();
-
m->mothurOutEndLine();
}