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

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b8956ecd6b495525d922c296484a433cd97ebdc9..cda2ef07da552d6ea4f25504e5b207a84d2594c7 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -69,7 +69,7 @@ SummarySharedCommand::SummarySharedCommand(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->getSharedFile()); //if user entered a file with a path then preserve it        
+                               outputDir += m->hasPath(globaldata->getSharedFile()); //if user entered a file with a path then preserve it     
                        }
 
                        //check for optional parameter and set defaults
@@ -77,7 +77,7 @@ SummarySharedCommand::SummarySharedCommand(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;  }
                        }
                        
@@ -92,17 +92,17 @@ SummarySharedCommand::SummarySharedCommand(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;
                        }
                        
                        string temp = validParameter.validFile(parameters, "all", false);                               if (temp == "not found") { temp = "false"; }
-                       all = isTrue(temp);
+                       all = m->isTrue(temp);
                        
                        if (abort == false) {
                        
@@ -157,8 +157,8 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                        }
                                }
                                
-                               outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary";
-                               openOutputFile(outputFileName, outputFileHandle);
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
+                               m->openOutputFile(outputFileName, outputFileHandle);
                                outputNames.push_back(outputFileName);
                                
                                mult = false;
@@ -239,8 +239,8 @@ int SummarySharedCommand::execute(){
                
                //create file and put column headers for multiple groups file
                if (mult == true) {
-                       outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
-                       openOutputFile(outAllFileName, outAll);
+                       outAllFileName = ((m->getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
+                       m->openOutputFile(outAllFileName, outAll);
                        outputNames.push_back(outAllFileName);
                        
                        outAll << "label" <<'\t' << "comparison" << '\t'; 
@@ -304,7 +304,7 @@ int SummarySharedCommand::execute(){
                                userLabels.erase(lookup[0]->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = lookup[0]->getLabel();
                                        
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }