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

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 43280edd76b1c924ed87572412977f682d3d7b17..23c0eaf0dd1852e9406fc600ce09ae8e80042431 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -46,7 +46,7 @@ GetListCountCommand::GetListCountCommand(string option)  {
                                it = parameters.find("list");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["list"] = inputDir + it->second;             }
                                }
@@ -70,7 +70,7 @@ GetListCountCommand::GetListCountCommand(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;  }
                        }
                        
@@ -160,7 +160,7 @@ int GetListCountCommand::execute(){
                                userLabels.erase(list->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = list->getLabel();
                                
                                delete list;
@@ -245,9 +245,9 @@ int GetListCountCommand::execute(){
 void GetListCountCommand::process(ListVector* list) {
        try {
                string binnames;
-               if (outputDir == "") { outputDir += hasPath(listfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + list->getLabel() + ".otu";
-               openOutputFile(outputFileName, out);
+               if (outputDir == "") { outputDir += m->hasPath(listfile); }
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+               m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName);
                
                m->mothurOut(list->getLabel()); m->mothurOutEndLine();
@@ -262,7 +262,7 @@ void GetListCountCommand::process(ListVector* list) {
                                out << i+1 << '\t' << binnames << endl;
                        }else{ //sort = name
                                vector<string> names;
-                               splitAtComma(binnames, names);
+                               m->splitAtComma(binnames, names);
                                
                                for (int j = 0; j < names.size(); j++) {
                                        out << names[j] << '\t' << i+1 << endl;