X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;h=02e165e978dc071ba19808139060866d7e41388c;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=5d917372e5f88a5a45b762efc57ab388d80a4ebc;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 5d91737..02e165e 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -111,7 +111,7 @@ PCOACommand::PCOACommand(string option)  {
 				phylipfile = m->getPhylipFile(); 
 				if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setPhylipFile(phylipfile); }	
 			
 			filename = phylipfile;  
 			
@@ -172,7 +172,7 @@ int PCOACommand::execute(){
 		
 		output(fbase, names, G, d);
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 		
 		if (metric) {   
 			
@@ -180,13 +180,13 @@ int PCOACommand::execute(){
 							
 				vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
 				
-				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 				
 				double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
 				
 				m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
 				
-				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 			}
 		}