X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=71a2db9723c32a39ea8e158074fbfac8a29de1ca;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=04c3bd325edf89638503cdcb49c2842c75ed1d17;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 04c3bd3..71a2db9 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -25,7 +25,8 @@ vector<string> GetSeqsCommand::setParameters(){
 		CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-		
+		CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
+
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
 		return myArray;
@@ -81,6 +82,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 				
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -199,21 +201,24 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 					m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); 
 					abort = true;
 				} 
-			}	
+			}else { m->setAccnosFile(accnosfile); }	
 			
 			if (accnosfile2 == "not found") { accnosfile2 = ""; }
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
-			else if (fastafile == "not found") {  fastafile = "";  }	
+			else if (fastafile == "not found") {  fastafile = "";  }
+			else { m->setFastaFile(fastafile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { 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; }
@@ -222,14 +227,22 @@ GetSeqsCommand::GetSeqsCommand(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; }
 			else if (taxfile == "not found") {  taxfile = "";  }
+			else { m->setTaxonomyFile(taxfile); }
 			
 			qualfile = validParameter.validFile(parameters, "qfile", true);
 			if (qualfile == "not open") { abort = true; }
 			else if (qualfile == "not found") {  qualfile = "";  }
+			else { m->setQualFile(qualfile); }
+			
+			accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
+			if (accnosfile2 == "not open") { abort = true; }
+			else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
+			
 			
 			string usedDups = "true";
 			string temp = validParameter.validFile(parameters, "dups", false);	if (temp == "not found") { temp = "true"; usedDups = ""; }
@@ -823,7 +836,15 @@ int GetSeqsCommand::compareAccnos(){
 			in >> name;
 			
 			if (namesAccnos.count(name) == 0){ //name unique to accnos2
-				namesAccnos2.insert(name);
+				int pos = name.find_last_of('_');
+				string tempName = name;
+				if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
+				if (namesAccnos.count(tempName) == 0){
+					namesAccnos2.insert(name);
+				}else { //you are in both so erase
+					namesAccnos.erase(name);
+					namesDups.insert(name);
+				}
 			}else { //you are in both so erase
 				namesAccnos.erase(name);
 				namesDups.insert(name);