paralellized rarefaction.single

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index bb9a4fd58b7362eb1ed69216cdfa2aa16817b2c6..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);
@@ -56,7 +56,7 @@ RareFactCommand::RareFactCommand(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       
                        }
 
                        //make sure the user has already run the read.otu command
@@ -67,7 +67,7 @@ RareFactCommand::RareFactCommand(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;  }
                        }
                        
@@ -82,7 +82,7 @@ RareFactCommand::RareFactCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sobs";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
@@ -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");
@@ -144,7 +148,7 @@ int RareFactCommand::execute(){
                
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
-                       string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
+                       string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
                        globaldata->inputFileName = inputFileNames[p];
                        
                        if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
@@ -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;
                                        
@@ -243,14 +247,14 @@ int RareFactCommand::execute(){
                                        userLabels.erase(order->getLabel());
                                }
                                
-                               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;
                                        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;
                                
@@ -339,7 +343,7 @@ vector<string> RareFactCommand::parseSharedFile(string filename) {
                input = globaldata->ginput;
                vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
                
-               string sharedFileRoot = getRootName(filename);
+               string sharedFileRoot = m->getRootName(filename);
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
@@ -358,7 +362,7 @@ vector<string> RareFactCommand::parseSharedFile(string filename) {
                
                        for (int i = 0; i < lookup.size(); i++) {
                                RAbundVector rav = lookup[i]->getRAbundVector();
-                               openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+                               m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
                                rav.print(*(filehandles[lookup[i]->getGroup()]));
                                (*(filehandles[lookup[i]->getGroup()])).close();
                        }