X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cooccurrencecommand.cpp;h=00de4d6ee612439732207872eba327b8a03f699e;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=6363f2a0bafec54c478317a6b33b44b336f95b2a;hpb=74ee6242ea65e88074c2b1df85c0f4428b79333b;p=mothur.git

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index 6363f2a..00de4d6 100644
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -51,6 +51,26 @@ string CooccurrenceCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string CooccurrenceCommand::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 == "summary") {  outputFileName =  "cooccurence.summary"; }
+            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, "CooccurrenceCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 CooccurrenceCommand::CooccurrenceCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -176,11 +196,11 @@ int CooccurrenceCommand::execute(){
 		set<string> userLabels = labels;
 
         ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
         m->openOutputFile(outputFileName, out);
         outputNames.push_back(outputFileName);  outputTypes["summary"].push_back(outputFileName);
         out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-        out << "metric\tlabel\tScore\tzScore\n";
+        out << "metric\tlabel\tScore\tzScore\tstandardDeviation\n";
 
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -272,6 +292,12 @@ int CooccurrenceCommand::execute(){
 int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
     try {
         int numOTUS = thisLookUp[0]->getNumBins();
+        
+        if(numOTUS < 2) {
+            m->mothurOut("Not enough OTUs for co-occurrence analysis, skipping"); m->mothurOutEndLine();
+            return 0;
+        }
+        
         vector< vector<int> > co_matrix; co_matrix.resize(thisLookUp[0]->getNumBins());
         for (int i = 0; i < thisLookUp[0]->getNumBins(); i++) { co_matrix[i].resize((thisLookUp.size()), 0); }
         vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
@@ -543,7 +569,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         
         m->mothurOut("zscore: " + toString(zscore)); m->mothurOutEndLine();
         m->mothurOut("standard deviation: " + toString(sd)); m->mothurOutEndLine();
-        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << endl;
+        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << '\t' << sd << endl;
         
         return 0;
     }