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

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index bb9a4fd58b7362eb1ed69216cdfa2aa16817b2c6..73d09b1206647cf832a06ec583e3a1d8d3956e2d 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -56,7 +56,7 @@ RareFactCommand::RareFactCommand(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
@@ -67,7 +67,7 @@ RareFactCommand::RareFactCommand(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 @@ RareFactCommand::RareFactCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sobs";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
@@ -144,7 +144,7 @@ int RareFactCommand::execute(){
                
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
-                       string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
+                       string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
                        globaldata->inputFileName = inputFileNames[p];
                        
                        if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
@@ -243,7 +243,7 @@ int RareFactCommand::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;
@@ -339,7 +339,7 @@ vector<string> RareFactCommand::parseSharedFile(string filename) {
                input = globaldata->ginput;
                vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
                
-               string sharedFileRoot = getRootName(filename);
+               string sharedFileRoot = m->getRootName(filename);
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
@@ -358,7 +358,7 @@ vector<string> RareFactCommand::parseSharedFile(string filename) {
                
                        for (int i = 0; i < lookup.size(); i++) {
                                RAbundVector rav = lookup[i]->getRAbundVector();
-                               openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+                               m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
                                rav.print(*(filehandles[lookup[i]->getGroup()]));
                                (*(filehandles[lookup[i]->getGroup()])).close();
                        }