modified freq parameter be a percentage of numSeqs, added catchall command - not...

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 37b54d1b850dbd9e72ca56fe4e506fa9a78439b4..357bc8708289e37063d731315b7411c715a05f1a 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);
@@ -84,6 +84,9 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
                        globaldata->Groups = Groups;
                        
                        string temp;
+                       temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "0.10"; }
+                       convert(temp, freq); 
+                       
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
                        convert(temp, nIters); 
                        
@@ -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.  It is a percentage of the number of sequences.  By default it is set to 0.10, meaning 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");