paralellized rarefaction.single

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 73d09b1206647cf832a06ec583e3a1d8d3956e2d..ae28d230b419db28c36272e57fc38ac7e2feff65 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -40,7 +40,7 @@ RareFactCommand::RareFactCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"iters","freq","label","calc","abund","outputdir","inputdir"};
+                       string Array[] =  {"iters","freq","label","calc","abund","processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -93,6 +93,9 @@ RareFactCommand::RareFactCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
                        convert(temp, nIters); 
+                       
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
+                       convert(temp, processors);
                }
                
        }
@@ -107,8 +110,9 @@ void RareFactCommand::help(){
        try {
                m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
                m->mothurOut("The rarefaction.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
-               m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund.  No parameters are required. \n");
+               m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc, processors and abund.  No parameters are required. \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("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
                m->mothurOut("The rarefaction.single command should be in the following format: \n");
                m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
                m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
@@ -235,7 +239,7 @@ int RareFactCommand::execute(){
                                if(allLines == 1 || labels.count(order->getLabel()) == 1){
                                        
                                        m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                                       rCurve = new Rarefact(order, rDisplays);
+                                       rCurve = new Rarefact(order, rDisplays, processors);
                                        rCurve->getCurve(freq, nIters);
                                        delete rCurve;
                                        
@@ -250,7 +254,7 @@ int RareFactCommand::execute(){
                                        order = (input->getOrderVector(lastLabel));
                                        
                                        m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                                       rCurve = new Rarefact(order, rDisplays);
+                                       rCurve = new Rarefact(order, rDisplays, processors);
                                        rCurve->getCurve(freq, nIters);
                                        delete rCurve;
                                        
@@ -290,7 +294,7 @@ int RareFactCommand::execute(){
                                order = (input->getOrderVector(lastLabel));
                                
                                m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-                               rCurve = new Rarefact(order, rDisplays);
+                               rCurve = new Rarefact(order, rDisplays, processors);
                                rCurve->getCurve(freq, nIters);
                                delete rCurve;