X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=unifracunweightedcommand.cpp;h=7836eb682f19d444ae2ffb7f82fe538efdb7d933;hb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;hp=68c943cb4e4c57efcc23eafe45f0da47fa6d4495;hpb=f099fdc1e3a0d7b75d780a164e5bdb93496a7a1d;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 68c943c..7836eb6 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -21,7 +21,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"groups","iters","distance","random", "outputdir","inputdir"};
+			string Array[] =  {"groups","iters","distance","random", "processors","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -61,6 +61,9 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			temp = validParameter.validFile(parameters, "random", false);					if (temp == "not found") { temp = "f"; }
 			random = m->isTrue(temp);
 			
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = "1";				}
+			convert(temp, processors); 
+			
 			if (!random) {  iters = 0;  } //turn off random calcs
 			
 			//if user selects distance = true and no groups it won't calc the pairwise
@@ -156,14 +159,9 @@ int UnifracUnweightedCommand::execute() {
 			utreeScores.resize(numComp);  
 			UWScoreSig.resize(numComp); 
 
-			userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
+			userData = unweighted->getValues(T[i], processors, outputDir);  //userData[0] = unweightedscore
 			
-			if (m->control_pressed) { 
-				if (random) { delete output;  }
-				outSum.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }
-				return 0; 
-			}
+			if (m->control_pressed) { if (random) { delete output;  } outSum.close();  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }return 0; }
 			
 			//output scores for each combination
 			for(int k = 0; k < numComp; k++) {