X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.cpp;h=b5b01e7f97166ed80143d349b9ae8c340d53e654;hb=2ecee16fec29d4c525f740ec19b27962ca09c050;hp=4744424d426d61243894d4779fa60dcd20781be3;hpb=57b3c96832667c1b70d4d526331f52e3d49e8237;p=mothur.git

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 4744424..b5b01e7 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -60,6 +60,27 @@ string MetaStatsCommand::getHelpString(){
 		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 {
@@ -449,7 +470,7 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 			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];
@@ -483,25 +504,16 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 				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);