X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=e6dace8b796103804c16a4de86104cff0b05da4f;hb=8742edef7a51b82834289e570d336f5a81ba1f2b;hp=c03fcc1ac133572fc7d821816edadc0b1fc32ecb;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index c03fcc1..e6dace8 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -129,11 +129,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 					abort = true; 
 				}
 			}else if (taxonomyFileName == "not open") { abort = true; }	
+			else { m->setTaxonomyFile(taxonomyFileName); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
-			else { readNamesFile(); }	
+			else { readNamesFile(); m->setNameFile(namefile); }	
 			
 			//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"){	
@@ -214,7 +215,7 @@ int PhylotypeCommand::execute(){
 			
 			if (m->control_pressed) { 
 				outRabund.close(); outSabund.close(); outList.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }
 				delete tree; return 0; 
 			}
 			
@@ -285,7 +286,7 @@ int PhylotypeCommand::execute(){
 		delete tree;
 		
 		if (m->control_pressed) { 
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }
 			return 0; 
 		}