added list.seqs command

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 71bfaf1d0f79b4866cebe71309e058a61bd2535e..5914f156a1a01831ce7cf6d2f3c52696c529f466 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -29,7 +29,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"iters","line","label","calc","groups"};
+                       string Array[] =  {"iters","line","label","calc","groups", "jumble"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -92,6 +92,11 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
                        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; }
+                       else { jumble = false; }
+                       globaldata->jumble = jumble;
+                       
                        if (abort == false) {
                        
                                string fileNameRoot = getRootName(globaldata->inputFileName);
@@ -125,12 +130,12 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 void RareFactSharedCommand::help(){
        try {
                mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
-               mothurOut("The rarefaction.shared command parameters are label, line, iters, groups and calc.  No parameters are required, but you may not use \n");
+               mothurOut("The rarefaction.shared command parameters are label, line, iters, groups, jumble and calc.  No parameters are required, but you may not use \n");
                mothurOut("both the line and label parameters at the same time. The rarefaction command should be in the following format: \n");
-               mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups).\n");
-               mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, calc=sharedobserved).\n");
+               mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
+               mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
                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");
-               mothurOut("The default value for groups is all the groups in your groupfile.\n");
+               mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
                validCalculator->printCalc("sharedrarefaction", cout);
                mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
                mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");