moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 390f47f9fac6f255ce6e30fec4c7b2264e25cdad..a55edd04e1db2f2acd24f57862b4dffb51e0ab8e 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -52,7 +52,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -66,7 +66,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -82,7 +82,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -91,7 +91,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "jclass-thetayc";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        if (abort == false) {
                        
@@ -209,7 +209,7 @@ int MatrixOutputCommand::execute(){
                                userLabels.erase(lookup[0]->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = lookup[0]->getLabel();
                                
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
@@ -347,8 +347,8 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                                                }
                                        }
                                        
-                                       exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
-                                       openOutputFile(exportFileName, out);
+                                       exportFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+                                       m->openOutputFile(exportFileName, out);
                                        outputNames.push_back(exportFileName);
                                        
                                        printSims(out);