X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;h=9fec2496068950b4863448fe500b17cbc957670a;hb=36cea83f926066127bf856e7eae1a70ce7e796d0;hp=b72f4b669d43b4b44fa1c20df4812155aaff82fc;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index b72f4b6..9fec249 100644
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -169,12 +169,12 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
 			
 			//check for required parameters			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
+			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); }
 			
@@ -193,7 +193,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
 			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(); }
@@ -220,7 +220,12 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
 			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 ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }			
-
+			
+			if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+				vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
+			
 		}
 
 	}
@@ -555,7 +560,8 @@ int RemoveLineageCommand::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]);
 			}
 		}
 		
@@ -577,7 +583,8 @@ int RemoveLineageCommand::readTax(){
 					
 					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 +616,8 @@ int RemoveLineageCommand::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]);
@@ -726,29 +734,6 @@ vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
 		exit(1);
 	}
 }
-/**************************************************************************************************/
-string RemoveLineageCommand::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, "RemoveLineageCommand", "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 RemoveLineageCommand::readAlign(){