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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 40b911bb8c844ad252a714383ce93109772209a0..c0b8248e58981473b1f7bf70709863c36c68992b 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -79,7 +79,7 @@ CollectSharedCommand::CollectSharedCommand(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;  }
                        }
                        
@@ -94,12 +94,12 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                        }
                        globaldata->Groups = Groups;
                        
@@ -108,12 +108,12 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        convert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
-                       all = isTrue(temp);
+                       all = m->isTrue(temp);
                                                
                        if (abort == false) {
                                
-                               if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
-                               string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+                               if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); }
+                               string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
                                format = globaldata->getFormat();
                                int i;
                                
@@ -283,7 +283,7 @@ int CollectSharedCommand::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;