1.23.0

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index b493c962461b51df14a06ef51b579235d89ef181..b7aa7e5fcb3bcc809c89ac3cc82c1ecae9d6272a 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -178,14 +178,14 @@ MetaStatsCommand::MetaStatsCommand(string option) {
 
                        
                        string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "threshold", false);                        if (temp == "not found") { temp = "0.05"; }
-                       convert(temp, threshold); 
+                       m->mothurConvert(temp, threshold); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                }
 
        }
@@ -394,7 +394,7 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        //get set names
                        string setA = namesOfGroupCombos[c][0]; 
                        string setB = namesOfGroupCombos[c][1];
-               
+               //cout << setA << '\t' << setB << endl;
                        //get filename
                        string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
                        outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
@@ -425,7 +425,8 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                                }
                        }
                        
-                       //for (int i = 0; i < subset.size(); i++) { cout << subset[i]->getGroup() << endl; }
+                       //for (int i = 0; i < subset.size(); i++) { cout << designMap->getGroup(subset[i]->getGroup()) << endl; }
+                       //cout << setACount << endl;
                        
                        if ((setACount == 0) || (setBCount == 0))  { 
                                m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();