X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.cpp;h=c2be580bb73313c91322e903c87027dc5da405d9;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=fc173100942199c9f5f5ea1b400d0cb0ad978303;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index fc17310..c2be580 100644
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -168,16 +168,19 @@ GetLineageCommand::GetLineageCommand(string option)  {
 			
 			//check for required parameters			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
-			else if (fastafile == "not found") {  fastafile = "";  }	
+			if (fastafile == "not open") { fastafile = ""; abort = true; }
+			else if (fastafile == "not found") {  fastafile = "";  }
+			else { m->setFastaFile(fastafile); }
 			
 			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 { m->setNameFile(namefile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") {  groupfile = "";  }	
+			else { m->setGroupFile(groupfile); }
 			
 			alignfile = validParameter.validFile(parameters, "alignreport", true);
 			if (alignfile == "not open") { abort = true; }
@@ -186,14 +189,15 @@ GetLineageCommand::GetLineageCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") {  listfile = "";  }
+			else { m->setListFile(listfile); }
 			
 			taxfile = validParameter.validFile(parameters, "taxonomy", true);
-			if (taxfile == "not open") { abort = true; }
+			if (taxfile == "not open") { taxfile = ""; abort = true; }
 			else if (taxfile == "not found") {  				
 				taxfile = m->getTaxonomyFile(); 
 				if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setTaxonomyFile(taxfile); }
 			
 			string usedDups = "true";
 			string temp = validParameter.validFile(parameters, "dups", false);	
@@ -213,6 +217,11 @@ GetLineageCommand::GetLineageCommand(string option)  {
 			m->splitAtChar(taxons, listOfTaxons, '-');
 			
 			if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
+		
+			if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+				vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
 		}
 
 	}
@@ -239,7 +248,7 @@ int GetLineageCommand::execute(){
 		if (listfile != "")			{		readList();		}
 		
 		
-		if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+		if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 		
 		if (outputNames.size() != 0) {
 			m->mothurOutEndLine();
@@ -302,7 +311,7 @@ int GetLineageCommand::readFasta(){
 		
 		while(!in.eof()){
 		
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
@@ -347,7 +356,7 @@ int GetLineageCommand::readList(){
 		
 		while(!in.eof()){
 			
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 			//read in list vector
 			ListVector list(in);
@@ -422,7 +431,7 @@ int GetLineageCommand::readName(){
 		
 		while(!in.eof()){
 		
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 			in >> firstCol;				
 			in >> secondCol;
@@ -507,7 +516,7 @@ int GetLineageCommand::readGroup(){
 		
 		while(!in.eof()){
 
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 
 			in >> name;				//read from first column
@@ -560,14 +569,15 @@ int GetLineageCommand::readTax(){
 			if (hasConPos != string::npos) {  
 				taxonsHasConfidence[i] = true; 
 				searchTaxons[i] = getTaxons(listOfTaxons[i]); 
-				noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]);
+				noConfidenceTaxons[i] = listOfTaxons[i];
+				m->removeConfidences(noConfidenceTaxons[i]);
 			}
 		}
 		
 		
 		while(!in.eof()){
 
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 			in >> name;				//read from first column
 			in >> tax;			//read from second column
@@ -580,7 +590,8 @@ int GetLineageCommand::readTax(){
 				if (!taxonsHasConfidence[j]) {
 					int hasConfidences = tax.find_first_of('(');
 					if (hasConfidences != string::npos) { 
-						newtax = removeConfidences(tax);
+						newtax = tax;
+						m->removeConfidences(newtax);
 					}
 				
 					int pos = newtax.find(noConfidenceTaxons[j]);
@@ -609,7 +620,8 @@ int GetLineageCommand::readTax(){
 						string noNewTax = tax;
 						int hasConfidences = tax.find_first_of('(');
 						if (hasConfidences != string::npos) { 
-							noNewTax = removeConfidences(tax);
+							noNewTax = tax;
+							m->removeConfidences(noNewTax);
 						}
 					
 						int pos = noNewTax.find(noConfidenceTaxons[j]);
@@ -721,29 +733,6 @@ vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 		exit(1);
 	}
 }
-/**************************************************************************************************/
-string GetLineageCommand::removeConfidences(string tax) {
-	try {
-		
-		string taxon = "";
-		int taxLength = tax.length();
-		for(int i=0;i<taxLength;i++){
-			if(tax[i] == ';'){
-				taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
-				taxon += ";";
-			}
-			else{
-				taxon += tax[i];
-			}
-		}
-				
-		return taxon;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "GetLineageCommand", "removeConfidences");
-		exit(1);
-	}
-}
 //**********************************************************************************************************************
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 int GetLineageCommand::readAlign(){
@@ -770,7 +759,7 @@ int GetLineageCommand::readAlign(){
 		
 		while(!in.eof()){
 		
-			if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 
 			in >> name;				//read from first column