From: westcott <westcott>
Date: Wed, 4 Jan 2012 13:31:41 +0000 (+0000)
Subject: 1.23.0
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=0ca63a8165baa0afa459e644ebe140ba496d5ba0

1.23.0
---

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 960d702..f03a901 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -224,34 +224,29 @@ AlignCommand::AlignCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "ksize", false);		if (temp == "not found"){	temp = "8";				}
-			convert(temp, kmerSize); 
+			m->mothurConvert(temp, kmerSize); 
 			
 			temp = validParameter.validFile(parameters, "match", false);		if (temp == "not found"){	temp = "1.0";			}
-			convert(temp, match);  
+			m->mothurConvert(temp, match);  
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, misMatch);  
+			m->mothurConvert(temp, misMatch);  
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
-			convert(temp, gapOpen);  
+			m->mothurConvert(temp, gapOpen);  
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, gapExtend); 
+			m->mothurConvert(temp, gapExtend); 
 			
 			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, "flip", false);			if (temp == "not found"){	temp = "f";				}
 			flip = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
-			//this is so the threads can quickly load the reference data
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			#else
-				if (processors != 1) { save = true; }
-			#endif
 			rdb->save = save; 
 			if (save) { //clear out old references
 				rdb->clearMemory();
@@ -272,7 +267,7 @@ AlignCommand::AlignCommand(string option)  {
 			else {	if (save) {	rdb->setSavedReference(templateFileName);	}	}
 			
 			temp = validParameter.validFile(parameters, "threshold", false);	if (temp == "not found"){	temp = "0.50";			}
-			convert(temp, threshold); 
+			m->mothurConvert(temp, threshold); 
 			
 			search = validParameter.validFile(parameters, "search", false);		if (search == "not found"){	search = "kmer";		}
 			if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
@@ -923,7 +918,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
 			string extension = "";
 			if (i != 0) { extension = toString(i) + ".temp"; }
 			
-			alignData* tempalign = new alignData((alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
+			alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
 			pDataArray.push_back(tempalign);
 			processIDS.push_back(i);
 				
diff --git a/aligncommand.h b/aligncommand.h
index fa1bf57..7f5122a 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -79,6 +79,7 @@ private:
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
 struct alignData {
+	string templateFileName;
 	string alignFName; 
 	string reportFName; 
 	string accnosFName;
@@ -94,7 +95,8 @@ struct alignData {
 	int count, kmerSize, threadID;
 	
 	alignData(){}
-	alignData(string a, string r, string ac, string f, string al, string se, int ks, MothurOut* mout, unsigned long long st, unsigned long long en, bool fl, float ma, float misMa, float gapO, float gapE, float thr, int tid) {
+	alignData(string te, string a, string r, string ac, string f, string al, string se, int ks, MothurOut* mout, unsigned long long st, unsigned long long en, bool fl, float ma, float misMa, float gapO, float gapE, float thr, int tid) {
+		templateFileName = te;
 		alignFName = a;
 		reportFName = r;
 		accnosFName = ac;
@@ -145,7 +147,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 		
 		pDataArray->count = pDataArray->end;
 		
-		AlignmentDB* templateDB = new AlignmentDB("saved-silent", pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
+		AlignmentDB* templateDB = new AlignmentDB(templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
 		
 		//moved this into driver to avoid deep copies in windows paralellized version
 		Alignment* alignment;
diff --git a/amovacommand.cpp b/amovacommand.cpp
index de277ab..3ec14bf 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -136,11 +136,11 @@ AmovaCommand::AmovaCommand(string option) {
 
 			string temp = validParameter.validFile(parameters, "iters", false);
 			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "alpha", false);
 			if (temp == "not found") { temp = "0.05"; }
-			convert(temp, experimentwiseAlpha); 
+			m->mothurConvert(temp, experimentwiseAlpha); 
 		}
 	}
 	catch(exception& e) {
diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 50b6f28..1b6afe3 100644
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -138,11 +138,11 @@ AnosimCommand::AnosimCommand(string option) {
 			
 			string temp = validParameter.validFile(parameters, "iters", false);
 			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "alpha", false);
 			if (temp == "not found") { temp = "0.05"; }
-			convert(temp, experimentwiseAlpha); 
+			m->mothurConvert(temp, experimentwiseAlpha); 
 		}
 		
 	}
diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index d249421..de96574 100644
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -157,7 +157,7 @@ BootSharedCommand::BootSharedCommand(string option) {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "iters", false);  if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 				
 			if (abort == false) {
 			
diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index ac1645d..1fc87db 100644
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -193,13 +193,13 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
 			
 			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, "window", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "25"; }
-			convert(temp, increment);
+			m->mothurConvert(temp, increment);
 		}
 	}
 	catch(exception& e) {
diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7468011..af6e33a 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -223,13 +223,13 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
 			
 			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, "window", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "numwanted", false);		if (temp == "not found") { temp = "20"; }
-			convert(temp, numwanted);
+			m->mothurConvert(temp, numwanted);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 400a715..9f53b17 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -281,7 +281,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 
 			string 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, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -306,14 +306,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 			
 			
 			temp = validParameter.validFile(parameters, "ksize", false);			if (temp == "not found") { temp = "7"; }
-			convert(temp, ksize);
+			m->mothurConvert(temp, ksize);
 			
 			temp = validParameter.validFile(parameters, "svg", false);				if (temp == "not found") { temp = "F"; }
 			svg = m->isTrue(temp);
 			if (nameFileNames.size() != 0) { svg = true; }
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, increment);			
+			m->mothurConvert(temp, increment);			
 		}
 	}
 	catch(exception& e) {
diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 61970d5..8eaf536 100644
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -345,16 +345,16 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
 			
 			string 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, "cutoff", false);	if (temp == "not found"){	temp = "0.50";	}
-			convert(temp, cutoff);
+			m->mothurConvert(temp, cutoff);
 			
 			temp = validParameter.validFile(parameters, "alpha", false);	if (temp == "not found"){	temp = "-5.54";	}
-			convert(temp, alpha);
+			m->mothurConvert(temp, alpha);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);	if (temp == "not found"){	temp = "0.33";	}
-			convert(temp, beta);
+			m->mothurConvert(temp, beta);
 		}
 	}
 	catch(exception& e) {
diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 0627793..3eb6589 100644
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -225,13 +225,13 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
 			
 			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, "window", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "25"; }
-			convert(temp, increment);
+			m->mothurConvert(temp, increment);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 0512be1..cfcad15 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -383,7 +383,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 			
 			string 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, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -441,34 +441,34 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 			
 			
 			temp = validParameter.validFile(parameters, "ksize", false);			if (temp == "not found") { temp = "7"; }
-			convert(temp, ksize);
+			m->mothurConvert(temp, ksize);
 						
 			temp = validParameter.validFile(parameters, "window", false);			if (temp == "not found") { temp = "50"; }			
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "match", false);			if (temp == "not found") { temp = "5"; }
-			convert(temp, match);
+			m->mothurConvert(temp, match);
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);			if (temp == "not found") { temp = "-4"; }
-			convert(temp, mismatch);
+			m->mothurConvert(temp, mismatch);
 			
 			temp = validParameter.validFile(parameters, "divergence", false);		if (temp == "not found") { temp = "1.007"; }
-			convert(temp, divR);
+			m->mothurConvert(temp, divR);
 			
 			temp = validParameter.validFile(parameters, "minsim", false);			if (temp == "not found") { temp = "90"; }
-			convert(temp, minSimilarity);
+			m->mothurConvert(temp, minSimilarity);
 			
 			temp = validParameter.validFile(parameters, "mincov", false);			if (temp == "not found") { temp = "70"; }
-			convert(temp, minCoverage);
+			m->mothurConvert(temp, minCoverage);
 			
 			temp = validParameter.validFile(parameters, "minbs", false);			if (temp == "not found") { temp = "90"; }
-			convert(temp, minBS);
+			m->mothurConvert(temp, minBS);
 			
 			temp = validParameter.validFile(parameters, "minsnp", false);			if (temp == "not found") { temp = "10"; }
-			convert(temp, minSNP);
+			m->mothurConvert(temp, minSNP);
 
 			temp = validParameter.validFile(parameters, "parents", false);			if (temp == "not found") { temp = "3"; }
-			convert(temp, parents); 
+			m->mothurConvert(temp, parents); 
 			
 			temp = validParameter.validFile(parameters, "realign", false);			if (temp == "not found") { temp = "t"; }
 			realign = m->isTrue(temp); 
@@ -482,13 +482,13 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 			search = validParameter.validFile(parameters, "search", false);			if (search == "not found") { search = "blast"; }
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }		
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			 
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "5"; }
-			convert(temp, increment);
+			m->mothurConvert(temp, increment);
 			
 			temp = validParameter.validFile(parameters, "numwanted", false);		if (temp == "not found") { temp = "15"; }		
-			convert(temp, numwanted);
+			m->mothurConvert(temp, numwanted);
 			
 			blastlocation = validParameter.validFile(parameters, "blastlocation", false);	
 			if (blastlocation == "not found") { blastlocation = ""; }
diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 40b3f26..01289a0 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 				
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			abskew = validParameter.validFile(parameters, "abskew", false);	if (abskew == "not found"){	useAbskew = false;  abskew = "1.9";	}else{  useAbskew = true;  }
 			if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index abfd8dc..68576cd 100644
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -121,7 +121,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(fastafile);	}
 			
 			string temp = validParameter.validFile(parameters, "numbases", false);	if (temp == "not found") { temp = "0"; } 
-			convert(temp, numbases);   
+			m->mothurConvert(temp, numbases);   
 			
 			temp = validParameter.validFile(parameters, "countgaps", false);	if (temp == "not found") { temp = "f"; } 
 			countGaps = m->isTrue(temp);  
diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index f36631a..e28961b 100644
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -206,7 +206,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
 			if ((basis != "otu") && (basis != "sequence")) { m->mothurOut("Invalid option for basis. basis options are otu and sequence, using otu."); m->mothurOutEndLine(); }
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "51"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "probs", false);					if (temp == "not found"){	temp = "true";			}
 			probs = m->isTrue(temp);
diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index af6d914..9ee7b5e 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -374,19 +374,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "ksize", false);		if (temp == "not found"){	temp = "8";				}
-			convert(temp, kmerSize); 
+			m->mothurConvert(temp, kmerSize); 
 			
 			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, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
-			//this is so the threads can quickly load the reference data
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			#else
-			if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
-			#endif
 			rdb->save = save; 
 			if (save) { //clear out old references
 				rdb->clearMemory();	
@@ -425,28 +420,28 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found"){	method = "bayesian";	}
 			
 			temp = validParameter.validFile(parameters, "match", false);		if (temp == "not found"){	temp = "1.0";			}
-			convert(temp, match);  
+			m->mothurConvert(temp, match);  
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, misMatch);  
+			m->mothurConvert(temp, misMatch);  
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
-			convert(temp, gapOpen);  
+			m->mothurConvert(temp, gapOpen);  
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, gapExtend); 
+			m->mothurConvert(temp, gapExtend); 
 			
 			temp = validParameter.validFile(parameters, "numwanted", false);	if (temp == "not found"){	temp = "10";			}
-			convert(temp, numWanted);
+			m->mothurConvert(temp, numWanted);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, cutoff);
+			m->mothurConvert(temp, cutoff);
 			
 			temp = validParameter.validFile(parameters, "probs", false);		if (temp == "not found"){	temp = "true";			}
 			probs = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "iters", false);		if (temp == "not found") { temp = "100";			}
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 
 
 			
diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index eef96ff..0e21a20 100644
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -157,8 +157,8 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
 		
 		//make classify
 		Classify* myclassify;
-		if(pDataArray->method == "bayesian"){	myclassify = new Bayesian("saved", "saved", pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID);		}
-		else if(pDataArray->method == "knn"){	myclassify = new Knn("saved", "saved", pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID);				}
+		if(pDataArray->method == "bayesian"){	myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID);		}
+		else if(pDataArray->method == "knn"){	myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID);				}
 		else {
 			pDataArray->m->mothurOut(pDataArray->search + " is not a valid method option. I will run the command using bayesian.");
 			pDataArray->m->mothurOutEndLine();
diff --git a/clustercommand.cpp b/clustercommand.cpp
index 47f5531..528f71c 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -183,7 +183,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
@@ -193,7 +193,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			method = validParameter.validFile(parameters, "method", false);
diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 0d57e68..603bd73 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -146,11 +146,11 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 8d2d3ea..ad1bd81 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -152,10 +152,10 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "diffs", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, diffs); 
+			m->mothurConvert(temp, diffs); 
 			
 			temp = validParameter.validFile(parameters, "percent", false);		if (temp == "not found"){	temp = "0";				}
-			convert(temp, percent);
+			m->mothurConvert(temp, percent);
 			
 		}
 				
diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 7505ae6..787d84a 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -264,7 +264,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
@@ -274,7 +274,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			
 			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, "splitmethod", false);	
 			if (splitmethod != "fasta") {
@@ -283,11 +283,11 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			}
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found")  { temp = "0.25"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			temp = validParameter.validFile(parameters, "taxlevel", false);		if (temp == "not found")  { temp = "3"; }
-			convert(temp, taxLevelCutoff); 
+			m->mothurConvert(temp, taxLevelCutoff); 
 			
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found") { method = "average"; }
 			
diff --git a/collectcommand.cpp b/collectcommand.cpp
index a65b417..e0d62dd 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -280,13 +280,13 @@ CollectCommand::CollectCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, size); 
+			m->mothurConvert(temp, size); 
 		}
 		
 	}
diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index a5721b0..f3a320b 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -274,7 +274,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "all", false);				if (temp == "not found") { temp = "false"; }
 			all = m->isTrue(temp);
diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index e32867f..4f8c53b 100644
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -159,7 +159,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "cutoff", false);  if (temp == "not found") { temp = "100"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			//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"){	outputDir = m->hasPath(fastafile);	}
diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index b943aa4..4e9c3c6 100644
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -187,7 +187,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
 			}
 			string temp;
 			temp = validParameter.validFile(parameters, "numaxes", false);		if (temp == "not found"){	temp = "3";				}
-			convert(temp, numaxes); 
+			m->mothurConvert(temp, numaxes); 
 			
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found"){	method = "pearson";		}
 			
diff --git a/distancecommand.cpp b/distancecommand.cpp
index 0f067ae..65edcf7 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -179,11 +179,11 @@ DistanceCommand::DistanceCommand(string option) {
 			convert(temp, countends); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if(temp == "not found"){	temp = "1.0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			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, "compress", false);		if(temp == "not found"){  temp = "F"; }
 			convert(temp, compress);
diff --git a/engine.cpp b/engine.cpp
index 670af78..ea1c0e1 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -186,11 +186,13 @@ bool InteractEngine::getInput(){
 					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
 					mout->currentBinLabels.clear();
 					mout->binLabelsInFile.clear();
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -370,12 +372,14 @@ bool BatchEngine::getInput(){
 					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
 					mout->currentBinLabels.clear();
 					mout->binLabelsInFile.clear();
 
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -537,12 +541,13 @@ bool ScriptEngine::getInput(){
 					mout->names.clear();
 					mout->saveNextLabel = "";
 					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
 					mout->currentBinLabels.clear();
 					mout->binLabelsInFile.clear();
 
-							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 					
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index d17f6a3..82c73f3 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -222,7 +222,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			vertical = validParameter.validFile(parameters, "vertical", false);		
 			if (vertical == "not found") { 
diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 2f6f810..35437e7 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -297,10 +297,10 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
 			if ((weighted) && (namefile == "")) { m->mothurOut("You cannot set weighted to true unless you provide a namesfile."); m->mothurOutEndLine(); abort = true; }
 			
 			temp = validParameter.validFile(parameters, "precision", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "10.0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));
 		}
 	}
diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index b2af034..4713693 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -182,14 +182,14 @@ HClusterCommand::HClusterCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0)); 
 			
 			method = validParameter.validFile(parameters, "method", false);
diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 57c4c86..7d9b482 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -226,10 +226,10 @@ HeatMapCommand::HeatMapCommand(string option) {
 			}
 			
 			string temp = validParameter.validFile(parameters, "numotu", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, numOTU);
+			m->mothurConvert(temp, numOTU);
 			
 			temp = validParameter.validFile(parameters, "fontsize", false);				if (temp == "not found") { temp = "24"; }
-			convert(temp, fontSize);
+			m->mothurConvert(temp, fontSize);
 			
 			sorted = validParameter.validFile(parameters, "sorted", false);				
 			if (sorted == "not found") { 
diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index d78b3cf..de35075 100644
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -242,7 +242,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "fontsize", false);				if (temp == "not found") { temp = "24"; }
-			convert(temp, fontsize);
+			m->mothurConvert(temp, fontsize);
 			
 			if (abort == false) {
 				ValidCalculators validCalculator;
diff --git a/homovacommand.cpp b/homovacommand.cpp
index 1869004..9b7ec9f 100644
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -139,11 +139,11 @@ HomovaCommand::HomovaCommand(string option) {
 			
 			string temp = validParameter.validFile(parameters, "iters", false);
 			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "alpha", false);
 			if (temp == "not found") { temp = "0.05"; }
-			convert(temp, experimentwiseAlpha); 
+			m->mothurConvert(temp, experimentwiseAlpha); 
 		}
 		
 	}
diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 40d3bcd..1864f74 100644
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -175,11 +175,11 @@ IndicatorCommand::IndicatorCommand(string option)  {
 			if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }	
 			
 			string temp = validParameter.validFile(parameters, "iters", false);		if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			if ((relabundfile == "") && (sharedfile == "")) { 
 				//is there are current file available for either of these?
diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 1e8102f..1d1d41f 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -170,13 +170,13 @@ LibShuffCommand::LibShuffCommand(string option)  {
 				
 			string temp;
 			temp = validParameter.validFile(parameters, "iters", false);				if (temp == "not found") { temp = "10000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "1.0"; }
-			convert(temp, cutOff); 
+			m->mothurConvert(temp, cutOff); 
 			
 			temp = validParameter.validFile(parameters, "step", false);				if (temp == "not found") { temp = "0.01"; }
-			convert(temp, step); 
+			m->mothurConvert(temp, step); 
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index c3ab352..409eae4 100644
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -125,7 +125,7 @@ MantelCommand::MantelCommand(string option)  {
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found"){	method = "pearson";		}
 			
 			string temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters);
+			m->mothurConvert(temp, iters);
 			
 			if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
 		}
diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index f5737c7..d1cf54b 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -186,7 +186,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 				
 			calc = validParameter.validFile(parameters, "calc", false);			
 			if (calc == "not found") { calc = "jclass-thetayc";  }
diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 0ff8b3f..b7aa7e5 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -178,14 +178,14 @@ MetaStatsCommand::MetaStatsCommand(string option) {
 
 			
 			string temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "threshold", false);			if (temp == "not found") { temp = "0.05"; }
-			convert(temp, threshold); 
+			m->mothurConvert(temp, threshold); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 		}
 
 	}
diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index f0886c8..9c45afe 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -149,10 +149,10 @@ MGClusterCommand::MGClusterCommand(string option) {
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
 			precisionLength = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "0.70"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));
 			
 			method = validParameter.validFile(parameters, "method", false);
@@ -162,10 +162,10 @@ MGClusterCommand::MGClusterCommand(string option) {
 			else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 
 			temp = validParameter.validFile(parameters, "length", false);			if (temp == "not found") { temp = "5"; }
-			convert(temp, length); 
+			m->mothurConvert(temp, length); 
 			
 			temp = validParameter.validFile(parameters, "penalty", false);			if (temp == "not found") { temp = "0.10"; }
-			convert(temp, penalty); 
+			m->mothurConvert(temp, penalty); 
 			
 			temp = validParameter.validFile(parameters, "min", false);				if (temp == "not found") { temp = "true"; }
 			minWanted = m->isTrue(temp); 
diff --git a/mothurout.cpp b/mothurout.cpp
index c58e634..9dcdc80 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1514,6 +1514,84 @@ int MothurOut::mothurRemove(string filename){
 		exit(1);
 	}
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool MothurOut::isNumeric1(string stringToCheck){
+	try {
+		bool numeric = false;
+		
+		if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+			
+		return numeric;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "isNumeric1");
+		exit(1);
+	}
+	
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 vector<vector<double> > MothurOut::binomial(int maxOrder){
diff --git a/mothurout.h b/mothurout.h
index 5ba3d08..d2a36b3 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -53,7 +53,7 @@ class MothurOut {
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode;
-		bool printedHeaders;
+		bool printedHeaders, commandInputsConvertError;
 		
 		//functions from mothur.h
 		//file operations
@@ -84,6 +84,9 @@ class MothurOut {
 		int readNames(string, map<string, vector<string> >&);
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		int mothurRemove(string);
+		bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+		bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+		bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 	
 		
 		//searchs and checks
@@ -97,6 +100,7 @@ class MothurOut {
 		int getNumChar(string, char);
 		bool isTrue(string);
 		bool isContainingOnlyDigits(string);
+		bool isNumeric1(string);
 	
 		
 		//string manipulation
@@ -198,6 +202,7 @@ class MothurOut {
 			flowfile = "";
 			gui = false;
 			printedHeaders = false;
+			commandInputsConvertError = false;
 			sharedHeaderMode = "";
 		}
 		~MothurOut();
diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index da82784..1d936d4 100644
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -141,19 +141,19 @@ NMDSCommand::NMDSCommand(string option)  {
 			}
 			
 			string temp = validParameter.validFile(parameters, "mindim", false);	if (temp == "not found") {	temp = "2";	}
-			convert(temp, mindim);
+			m->mothurConvert(temp, mindim);
 			
 			temp = validParameter.validFile(parameters, "maxiters", false);	if (temp == "not found") {	temp = "500";	}
-			convert(temp, maxIters);
+			m->mothurConvert(temp, maxIters);
 			
 			temp = validParameter.validFile(parameters, "iters", false);	if (temp == "not found") {	temp = "10";	}
-			convert(temp, iters);
+			m->mothurConvert(temp, iters);
 			
 			temp = validParameter.validFile(parameters, "maxdim", false);	if (temp == "not found") {	temp = "2";	}
-			convert(temp, maxdim);
+			m->mothurConvert(temp, maxdim);
 			
 			temp = validParameter.validFile(parameters, "epsilon", false);	if (temp == "not found") {	temp = "0.000000000001";	}
-			convert(temp, epsilon); 
+			m->mothurConvert(temp, epsilon); 
 			
 			if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 			if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 43c8e22..bbf9a83 100644
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -176,7 +176,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
 			if (temp == "not found") {  
 				norm = 0;  //once you have read, set norm to smallest group number
 			}else { 
-				convert(temp, norm);
+				m->mothurConvert(temp, norm);
 				if (norm < 0) { m->mothurOut("norm must be positive."); m->mothurOutEndLine(); abort=true; }
 			}
 			
diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 2245ac9..114f545 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -212,23 +212,23 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
 			// ...at some point should added some additional type checking...
 			string temp;
 			temp = validParameter.validFile(parameters, "match", false);		if (temp == "not found"){	temp = "1.0";			}
-			convert(temp, match);  
+			m->mothurConvert(temp, match);  
 			
 			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, misMatch);  
+			m->mothurConvert(temp, misMatch);  
 			
 			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
-			convert(temp, gapOpen);  
+			m->mothurConvert(temp, gapOpen);  
 			
 			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
-			convert(temp, gapExtend); 
+			m->mothurConvert(temp, gapExtend); 
 			
 			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, "cutoff", false);		if(temp == "not found"){	temp = "1.0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "countends", false);	if(temp == "not found"){	temp = "T";	}
 			countends = m->isTrue(temp); 
diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 3752935..ccf2952 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -171,11 +171,11 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			}
 				
 			itersString = validParameter.validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
-			convert(itersString, iters); 
+			m->mothurConvert(itersString, iters); 
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 		}
 
diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index ca0d02a..69c7b30 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -167,10 +167,10 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "rarefy", false);			if (temp == "not found") { temp = "F"; }
 			rarefy = m->isTrue(temp);
@@ -187,7 +187,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = "";  }
diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index e6dace8..00f960b 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -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; }
diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 898ad9b..968ba4f 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -180,7 +180,7 @@ PipelineCommand::PipelineCommand(string option) {
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			if (pipeFilename != "") {
 				abort = readUsersPipeline();
diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index cf42568..cac80b8 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -156,11 +156,11 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else {   m->setGroupFile(groupfile); bygroup = true;  }
 			
 			string temp	= validParameter.validFile(parameters, "diffs", false);		if(temp == "not found"){	temp = "1"; }
-			convert(temp, diffs); 
+			m->mothurConvert(temp, diffs); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			
 		}
@@ -372,6 +372,9 @@ int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newF
 		
 		//append output files
 		for(int i=0;i<processIDS.size();i++){
+			newFName = m->getFullPathName(".\\" + newFName);
+			newNName = m->getFullPathName(".\\" + newNName);
+			cout << newFName << endl;
 			m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 			m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 			
diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 8d1cfc8..b8c1c6f 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -253,17 +253,17 @@ RareFactCommand::RareFactCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "abund", false);			if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, nIters); 
+			m->mothurConvert(temp, nIters); 
 			
 			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, "groupmode", false);		if (temp == "not found") { temp = "T"; }
 			groupMode = m->isTrue(temp);
diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index b0d6650..64bdbb4 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -162,10 +162,10 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, nIters); 
+			m->mothurConvert(temp, nIters); 
 			
 			temp = validParameter.validFile(parameters, "jumble", false);			if (temp == "not found") { temp = "T"; }
 			if (m->isTrue(temp)) { jumble = true; }
diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 788bdcb..8bf6996 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -121,7 +121,7 @@ ReadDistCommand::ReadDistCommand(string option) {
 			//get user cutoff and precision or use defaults
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 351ace6..24b6165 100644
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -220,7 +220,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "nseqs", false);	 
 			if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
-			else { convert(temp, nseqs); }
+			else { m->mothurConvert(temp, nseqs); }
 			
 			temp = validParameter.validFile(parameters, "bygroup", false);	 if (temp == "not found") { temp = "f"; }
 			byGroup = m->isTrue(temp);
diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index ec2d8e0..16618f7 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 +259,7 @@ 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); 
 		}
 
 	}
diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 2fb2efb..82922ed 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -183,11 +183,11 @@ SensSpecCommand::SensSpecCommand(string option)  {
 //			cout << "name:\t" << nameFile << endl;
 
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found") { temp = "-1.00"; }
-			convert(temp, cutoff);  
+			m->mothurConvert(temp, cutoff);  
 //			cout << cutoff << endl;
 			
 			temp = validParameter.validFile(parameters, "precision", false);	if (temp == "not found") { temp = "100"; }
-			convert(temp, precision);  
+			m->mothurConvert(temp, precision);  
 //			cout << precision << endl;
 			
 			string label = validParameter.validFile(parameters, "label", false);			
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 253e03e..9ac7c5b 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -213,7 +213,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			temp = validParameter.validFile(parameters, "threshold", false);	if (temp == "not found") { temp = "1.00"; }
-			convert(temp, threshold);  
+			m->mothurConvert(temp, threshold);  
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -242,7 +242,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 
 			substitutionMatrix.resize(6);
 			for(int i=0;i<6;i++){	substitutionMatrix[i].resize(6,0);	}
diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index eeba041..93950d1 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -131,7 +131,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 
 
 		}
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 13e7ccf..e266b98 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -251,19 +251,19 @@ ShhherCommand::ShhherCommand(string option) {
 			
 			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, "cutoff", false);	if (temp == "not found"){	temp = "0.01";		}
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "mindelta", false);	if (temp == "not found"){	temp = "0.000001";	}
-			convert(temp, minDelta); 
+			m->mothurConvert(temp, minDelta); 
 
 			temp = validParameter.validFile(parameters, "maxiter", false);	if (temp == "not found"){	temp = "1000";		}
-			convert(temp, maxIters); 
+			m->mothurConvert(temp, maxIters); 
 
 			temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")	{	temp = "60";		}
-			convert(temp, sigma); 
+			m->mothurConvert(temp, sigma); 
 			
 			flowOrder = validParameter.validFile(parameters, "order", false);
 			if (flowOrder == "not found"){ flowOrder = "TACG";		}
diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 8ef4c8c..6a339b8 100644
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -37,7 +37,7 @@ string ShhhSeqsCommand::getHelpString(){
 		string helpString = "";
 		helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
 		helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
-		helpString += "The fasta parameter allows you to enter the fasta file containing your potentially sequences, and is required, unless you have a valid current fasta file. \n";
+		helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
 		helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
 		helpString += "The group parameter allows you to provide a group file.  When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
 		helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
@@ -160,11 +160,11 @@ ShhhSeqsCommand::ShhhSeqsCommand(string option) {
 			else {   m->setGroupFile(groupfile);  }
 			
 			string temp	= validParameter.validFile(parameters, "sigma", false);		if(temp == "not found"){	temp = "0.01"; }
-			convert(temp, sigma); 
+			m->mothurConvert(temp, sigma); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 		}
 	}
 	catch(exception& e) {
diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 140f379..989ef59 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -213,7 +213,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 			accnos = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "0"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 
 			if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
 
diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 24c83fd..fe9e934 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -234,7 +234,7 @@ SubSampleCommand::SubSampleCommand(string option) {
 			}
 			
 			string temp = validParameter.validFile(parameters, "size", false);		if (temp == "not found"){	temp = "0";		}
-			convert(temp, size);  
+			m->mothurConvert(temp, size);  
 			
 			temp = validParameter.validFile(parameters, "persample", false);		if (temp == "not found"){	temp = "f";		}
 			persample = m->isTrue(temp);
diff --git a/summarycommand.cpp b/summarycommand.cpp
index 629750b..022b174 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -231,10 +231,10 @@ SummaryCommand::SummaryCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, size); 
+			m->mothurConvert(temp, size); 
 			
 			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "T"; }
 			groupMode = m->isTrue(temp);
diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 0969a12..421a8f2 100644
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -131,7 +131,7 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);			
+			m->mothurConvert(temp, processors);			
 		}
 	}
 	catch(exception& e) {
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index c8d112f..7116e46 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -205,7 +205,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			if (abort == false) {
 			
diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 3a8cd26..8c5aa4b 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -257,10 +257,10 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index c2ea534..77dacfe 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -149,10 +149,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "minflows", false);	if (temp == "not found") { temp = "450"; }
-			convert(temp, minFlows);  
+			m->mothurConvert(temp, minFlows);  
 
 			temp = validParameter.validFile(parameters, "maxflows", false);	if (temp == "not found") { temp = "450"; }
-			convert(temp, maxFlows);  
+			m->mothurConvert(temp, maxFlows);  
 			
 			
 			temp = validParameter.validFile(parameters, "oligos", true);
@@ -164,28 +164,28 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 			else if(m->isTrue(temp))	{	fasta = 1;	}
 			
 			temp = validParameter.validFile(parameters, "maxhomop", false);		if (temp == "not found"){	temp = "9";		}
-			convert(temp, maxHomoP);  
+			m->mothurConvert(temp, maxHomoP);  
 
 			temp = validParameter.validFile(parameters, "signal", false);		if (temp == "not found"){	temp = "0.50";	}
-			convert(temp, signal);  
+			m->mothurConvert(temp, signal);  
 
 			temp = validParameter.validFile(parameters, "noise", false);		if (temp == "not found"){	temp = "0.70";	}
-			convert(temp, noise);  
+			m->mothurConvert(temp, noise);  
 	
 			temp = validParameter.validFile(parameters, "bdiffs", false);		if (temp == "not found"){	temp = "0";		}
-			convert(temp, bdiffs);
+			m->mothurConvert(temp, bdiffs);
 			
 			temp = validParameter.validFile(parameters, "pdiffs", false);		if (temp == "not found"){	temp = "0";		}
-			convert(temp, pdiffs);
+			m->mothurConvert(temp, pdiffs);
 			
 			temp = validParameter.validFile(parameters, "tdiffs", false);
 			if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
-			convert(temp, tdiffs);
+			m->mothurConvert(temp, tdiffs);
 			if(tdiffs == 0){	tdiffs = bdiffs + pdiffs;	}
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 	
 			flowOrder = validParameter.validFile(parameters, "order", false);
 			if (flowOrder == "not found"){ flowOrder = "TACG";		}
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index b804c8f..213e241 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -213,25 +213,25 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			
 			
 			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 = "0"; }
-			convert(temp, maxHomoP);  
+			m->mothurConvert(temp, maxHomoP);  
 
 			temp = validParameter.validFile(parameters, "minlength", false);	if (temp == "not found") { temp = "0"; }
-			convert(temp, minLength); 
+			m->mothurConvert(temp, minLength); 
 			
 			temp = validParameter.validFile(parameters, "maxlength", false);	if (temp == "not found") { temp = "0"; }
-			convert(temp, maxLength);
+			m->mothurConvert(temp, maxLength);
 			
 			temp = validParameter.validFile(parameters, "bdiffs", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, bdiffs);
+			m->mothurConvert(temp, bdiffs);
 			
 			temp = validParameter.validFile(parameters, "pdiffs", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, pdiffs);
+			m->mothurConvert(temp, pdiffs);
 			
 			temp = validParameter.validFile(parameters, "tdiffs", false);		if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
-			convert(temp, tdiffs);
+			m->mothurConvert(temp, tdiffs);
 			
 			if(tdiffs == 0){	tdiffs = bdiffs + pdiffs;	}
 			
@@ -246,7 +246,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			else						{	nameFile = temp;	m->setNameFile(nameFile); }
 			
 			temp = validParameter.validFile(parameters, "qthreshold", false);	if (temp == "not found") { temp = "0"; }
-			convert(temp, qThreshold);
+			m->mothurConvert(temp, qThreshold);
 			
 			temp = validParameter.validFile(parameters, "qtrim", false);		if (temp == "not found") { temp = "t"; }
 			qtrim = m->isTrue(temp);
@@ -277,7 +277,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			
 			if(allFiles && (oligoFile == "")){
diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index c09301f..047d06e 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -171,7 +171,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			}
 				
 			itersString = validParameter.validFile(parameters, "iters", false);				if (itersString == "not found") { itersString = "1000"; }
-			convert(itersString, iters); 
+			m->mothurConvert(itersString, iters); 
 			
 			string temp = validParameter.validFile(parameters, "distance", false);			
 			if (temp == "not found") { phylip = false; outputForm = ""; }
@@ -188,7 +188,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			if (!random) {  iters = 0;  } //turn off random calcs
 			
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index bc9d0c5..b007db1 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -172,7 +172,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			}
 				
 			itersString = validParameter.validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
-			convert(itersString, iters); 
+			m->mothurConvert(itersString, iters); 
 			
 			string temp = validParameter.validFile(parameters, "distance", false);			
 			if (temp == "not found") { phylip = false; outputForm = ""; }
@@ -189,7 +189,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			if (!random) {  iters = 0;  } //turn off random calcs
 		}
diff --git a/venncommand.cpp b/venncommand.cpp
index b5b401d..1b4e3bc 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -193,7 +193,7 @@ VennCommand::VennCommand(string option)  {
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "nseqs", false);		if (temp == "not found"){	temp = "f";				}
 			nseqs = m->isTrue(temp); 
@@ -202,7 +202,7 @@ VennCommand::VennCommand(string option)  {
 			perm = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "fontsize", false);		if (temp == "not found") { temp = "24"; }
-			convert(temp, fontsize);
+			m->mothurConvert(temp, fontsize);
 
 		}