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

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 37b54d1b850dbd9e72ca56fe4e506fa9a78439b4..c0f5ec0c4daba141c9267817836522e0d22c1a3a 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -28,7 +28,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"iters","label","calc","groups", "jumble","outputdir","inputdir"};
+                       string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -50,7 +50,7 @@ RareFactSharedCommand::RareFactSharedCommand(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       
                        }
 
                        
@@ -59,7 +59,7 @@ RareFactSharedCommand::RareFactSharedCommand(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;  }
                        }
                        
@@ -74,27 +74,30 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sharedobserved";  }
                        }
-                       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 = "100"; }
+                       convert(temp, freq); 
+                       
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
                        convert(temp, nIters); 
                        
                        temp = validParameter.validFile(parameters, "jumble", false);                   if (temp == "not found") { temp = "T"; }
-                       if (isTrue(temp)) { jumble = true; }
+                       if (m->isTrue(temp)) { jumble = true; }
                        else { jumble = false; }
                        globaldata->jumble = jumble;
                        
                        if (abort == false) {
                        
-                               string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+                               string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
 //                             format = globaldata->getFormat();
 
                                
@@ -130,6 +133,7 @@ void RareFactSharedCommand::help(){
                m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc.  No parameters are required.\n");
                m->mothurOut("The rarefaction command should be in the following format: \n");
                m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\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");
                m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03,  iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
                m->mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
@@ -210,7 +214,7 @@ int RareFactSharedCommand::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];  }