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

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index ca8c8a66a9445c21a7472301dce1bce71abe34b3..ba05ea1e11d3e5e603ec84babe81ee172c68a440 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -39,7 +39,7 @@ GetSAbundCommand::GetSAbundCommand(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
@@ -50,7 +50,7 @@ GetSAbundCommand::GetSAbundCommand(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;  }
                        }
                        
@@ -61,8 +61,8 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                        }
                                
                        if (abort == false) {
-                               filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "sabund";
-                               openOutputFile(filename, out);
+                               filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
+                               m->openOutputFile(filename, out);
                        }
                }
 
@@ -133,7 +133,7 @@ int GetSAbundCommand::execute(){
                                        userLabels.erase(order->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = order->getLabel();
                                        
                                        delete order;