added modify names parameter to set.dir

[mothur.git] / cooccurrencecommand.cpp

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index e4c915d6a14e4a9755a17d64c073fdda1440803b..48fba8c9727b4df62b7a37cbb629a55c7c082d74 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -12,14 +12,14 @@
 //**********************************************************************************************************************
 vector<string> CooccurrenceCommand::setParameters() {  
        try { 
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);             
-               CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "",false,false); parameters.push_back(pmetric);
-               CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "",false,false); parameters.push_back(pmatrix);
-        CommandParameter pruns("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pruns);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-        CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);              
+               CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "","",false,false); parameters.push_back(pmetric);
+               CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "","",false,false); parameters.push_back(pmatrix);
+        CommandParameter pruns("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pruns);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
 
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -51,6 +51,21 @@ string CooccurrenceCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string CooccurrenceCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "summary") {  pattern = "[filename],cooccurence.summary"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CooccurrenceCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 CooccurrenceCommand::CooccurrenceCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -176,11 +191,13 @@ int CooccurrenceCommand::execute(){
                set<string> userLabels = labels;
 
         ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+               string outputFileName = getOutputFileName("summary", variables);
         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\tstandardDeviation\n";
+        out << "metric\tlabel\tScore\tzScore\tstandardDeviation\tnp_Pvalue\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))) {
@@ -301,11 +318,11 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         int nrows = numOTUS;//rows of inital matrix
         int ncols = thisLookUp.size();//groups
         double initscore = 0.0;
-        
+       
         vector<double> stats;
-        double probabilityMatrix[ncols * nrows];
+        vector<double> probabilityMatrix; probabilityMatrix.resize(ncols * nrows, 0);
         vector<vector<int> > nullmatrix(nrows, vector<int>(ncols, 0));
-        
+       
         TrialSwap2 trial;
         
         int n = accumulate( columntotal.begin(), columntotal.end(), 0 );
@@ -549,7 +566,8 @@ 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 << '\t' << sd << endl;
+        m->mothurOut("non-parametric p-value: " + toString(pvalue)); m->mothurOutEndLine();
+        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore << '\t' << sd << '\t' << pvalue << endl;
         
         return 0;
     }