X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=41067396c6f5333faeaf3346afd9b865ad351531;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=9a6998e28fdb7f41a8c7be6b00b86a7f0c5be8ee;hpb=88fbc534a92cb91900e98a3288dfa1f68828b69b;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 9a6998e..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);
+			}
 		}
 
 	}
@@ -283,10 +288,15 @@ int ScreenSeqsCommand::execute(){
 			getSummary(positions); 
 		} 
 		else { 
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			positions = m->divideFile(fastafile, processors);
 			for (int i = 0; i < (positions.size()-1); i++) {
 				lines.push_back(new linePair(positions[i], positions[(i+1)]));
-			}	
+			}
+			#else 
+				positions.push_back(0); positions.push_back(1000);
+				lines.push_back(new linePair(0, 1000));
+			#endif
 		}
 				
 		string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
@@ -659,12 +669,15 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 		vector<int> ambigBases;
 		vector<int> longHomoPolymer;
 		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		vector<unsigned long long> positions = m->divideFile(fastafile, processors);
-				
+		
 		for (int i = 0; i < (positions.size()-1); i++) {
 			lines.push_back(new linePair(positions[i], positions[(i+1)]));
 		}	
-		
+#else
+		lines.push_back(new linePair(0, 1000));
+#endif
 		
 #ifdef USE_MPI
 		int pid;
@@ -778,7 +791,7 @@ int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 				
 				count++;
 			}
-			
+			//if((count) % 100 == 0){	m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();		}
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }