X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=41067396c6f5333faeaf3346afd9b865ad351531;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=ec2d8e003a31a712de8c32d255d164b6b13cd46c;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index ec2d8e0..4106739 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -220,26 +220,26 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "start", false);		if (temp == "not found") { temp = "-1"; }
-			convert(temp, startPos); 
+			m->mothurConvert(temp, startPos); 
 		
 			temp = validParameter.validFile(parameters, "end", false);			if (temp == "not found") { temp = "-1"; }
-			convert(temp, endPos);  
+			m->mothurConvert(temp, endPos);  
 
 			temp = validParameter.validFile(parameters, "maxambig", false);		if (temp == "not found") { temp = "-1"; }
-			convert(temp, maxAmbig);  
+			m->mothurConvert(temp, maxAmbig);  
 
 			temp = validParameter.validFile(parameters, "maxhomop", false);		if (temp == "not found") { temp = "-1"; }
-			convert(temp, maxHomoP);  
+			m->mothurConvert(temp, maxHomoP);  
 
 			temp = validParameter.validFile(parameters, "minlength", false);	if (temp == "not found") { temp = "-1"; }
-			convert(temp, minLength); 
+			m->mothurConvert(temp, minLength); 
 			
 			temp = validParameter.validFile(parameters, "maxlength", false);	if (temp == "not found") { temp = "-1"; }
-			convert(temp, maxLength); 
+			m->mothurConvert(temp, maxLength); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			temp = validParameter.validFile(parameters, "optimize", false);	//optimizing trumps the optimized values original value
 			if (temp == "not found"){	temp = "none";		}
@@ -259,7 +259,12 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
 			if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 			
 			temp = validParameter.validFile(parameters, "criteria", false);	if (temp == "not found"){	temp = "90";				}
-			convert(temp, criteria); 
+			m->mothurConvert(temp, criteria); 
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 
 	}