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

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index b665c88cdede4273b1aadd5bf1d4ee21ddec6b85..b7dd7153609ada80c297d5d51cab70d3cae5ebc4 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -39,7 +39,7 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        string 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
@@ -50,12 +50,12 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
-                       sorted = isTrue(temp);
+                       sorted = m->isTrue(temp);
                        
                        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;  }
                        }
                        
@@ -66,8 +66,8 @@ GetRAbundCommand::GetRAbundCommand(string option)  {
                        }
                                
                        if (abort == false) {
-                               filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "rabund";
-                               openOutputFile(filename, out);
+                               filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund";
+                               m->openOutputFile(filename, out);
                        }
                }
 
@@ -141,7 +141,7 @@ int GetRAbundCommand::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;