paralellized phylo.diversity

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 78ce5c400221d5620fd85447627dcb7a3b658994..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;  }
                        }
                        
@@ -94,26 +94,26 @@ 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;
                        
                        string temp;
-                       temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "0.10"; }
+                       temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
                        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;
                                
@@ -208,7 +208,7 @@ void CollectSharedCommand::help(){
                m->mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
                m->mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
-               m->mothurOut("The freq parameter is used indicate when to output your data.  It is a percentage of the number of sequences.  By default it is set to 0.10, meaning 10%. \n");
+               m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
                validCalculator->printCalc("shared", cout);
                m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
@@ -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;