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

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index d174cdd7ddced16a34aeea406ae6397fca26496f..9424347180c7713c6b498fd16cada4e7e86accd4 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -52,7 +52,7 @@ BootSharedCommand::BootSharedCommand(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       
                        }
 
                        
@@ -67,7 +67,7 @@ BootSharedCommand::BootSharedCommand(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;  }
                        }
                        
@@ -80,7 +80,7 @@ BootSharedCommand::BootSharedCommand(string option) {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -89,7 +89,7 @@ BootSharedCommand::BootSharedCommand(string option) {
                        else { 
                                 if (calc == "default")  {  calc = "jclass-thetayc";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        string temp;
                        temp = validParameter.validFile(parameters, "iters", false);  if (temp == "not found") { temp = "1000"; }
@@ -232,7 +232,7 @@ int BootSharedCommand::execute(){
                        }
                        
                        //you have a label the user want that is smaller than this label and the last label has not already been processed
-                       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;
@@ -408,8 +408,8 @@ int BootSharedCommand::process(SharedOrderVector* order) {
                                //open an ostream for each calc to print to
                                for (int z = 0; z < treeCalculators.size(); z++) {
                                        //create a new filename
-                                       outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
-                                       openOutputFile(outputFile, *(out[z]));
+                                       outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
+                                       m->openOutputFile(outputFile, *(out[z]));
                                        outputNames.push_back(outputFile);
                                }
                                
@@ -487,7 +487,7 @@ int BootSharedCommand::process(SharedOrderVector* order) {
                                        //set global data to calc trees
                                        globaldata->gTree = trees[k];
                                        
-                                       string filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+                                       string filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
                                        consensus = new ConcensusCommand(filename);
                                        consensus->execute();
                                        delete consensus;