X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=1d6c391de69c83a86971873577a0df0b21efdbcd;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=ef23375df9425f11816acbf8594f46e613e9e148;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index ef23375..1d6c391 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -128,11 +128,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 					m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine(); 
 					abort = true; 
 				}
-			}else if (taxonomyFileName == "not open") { abort = true; }	
+			}else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }	
 			else { m->setTaxonomyFile(taxonomyFileName); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
 			else { readNamesFile(); m->setNameFile(namefile); }	
 			
@@ -144,7 +144,7 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "-1"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; allLines = 1; }
@@ -153,6 +153,11 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
 				else { allLines = 1;  }
 			}
 			
+			if (namefile == "") {
+				vector<string> files; files.push_back(taxonomyFileName);
+				parser.getNameFile(files);
+			}
+			
 		}
 	}
 	catch(exception& e) {
@@ -215,7 +220,7 @@ 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; 
 			}
 			
@@ -286,7 +291,7 @@ 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; 
 		}