X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=f35da2e46588829480a5540cdcd1148fd54e31bf;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=81722dd3e4047fc2505d64372a2ca539978c9445;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 81722dd..f35da2e 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -16,12 +16,12 @@
 //**********************************************************************************************************************
 vector<string> RemoveGroupsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-		CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared);
-		CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
-		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
+		CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
+		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
+		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
 		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -190,6 +190,11 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 			else if (namefile == "not found") {  namefile = "";  }	
 			else { m->setNameFile(namefile); }
 			
+			groupfile = validParameter.validFile(parameters, "group", true);
+			if (groupfile == "not open") { groupfile = "";  abort = true; }
+			else if (groupfile == "not found") {  	groupfile = "";		}
+			else { m->setGroupFile(groupfile); }	
+			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") {  listfile = "";  }
@@ -248,6 +253,12 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 			
 			if ((fastafile == "") && (namefile == "") && (groupfile == "")  && (sharedfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
 			if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")))  { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
+			
+			if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+				vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+				parser.getNameFile(files);
+			}
+		
 		}
 		
 	}
@@ -370,9 +381,16 @@ int RemoveGroupsCommand::readFasta(){
 				//if this name is in the accnos file
 				if (names.count(name) == 0) {
 					wroteSomething = true;
-					
-					currSeq.printSequence(out);
-				}else { removedCount++; }
+					currSeq.printSequence(out); 
+				}else { 
+					//if you are not in the accnos file check if you are a name that needs to be changed
+					map<string, string>::iterator it = uniqueToRedundant.find(name);
+					if (it != uniqueToRedundant.end()) {
+						wroteSomething = true;
+						currSeq.setName(it->second);
+						currSeq.printSequence(out);
+					}else { removedCount++; }
+				}
 			}
 			m->gobble(in);
 		}
@@ -518,12 +536,23 @@ int RemoveGroupsCommand::readList(){
 					
 					//if that name is in the .accnos file, add it
 					if (names.count(name) == 0) {  newNames += name + ",";  }
-					else { removedCount++; }
+					else {
+						//if you are not in the accnos file check if you are a name that needs to be changed
+						map<string, string>::iterator it = uniqueToRedundant.find(name);
+						if (it != uniqueToRedundant.end()) {
+							newNames += it->second + ",";
+						}else { removedCount++; }
+					}
 				}
 				
 				//get last name
 				if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
-				else { removedCount++; }
+				else { //if you are not in the accnos file check if you are a name that needs to be changed
+					map<string, string>::iterator it = uniqueToRedundant.find(binnames);
+					if (it != uniqueToRedundant.end()) {
+						newNames += it->second + ",";
+					}else { removedCount++; }
+				}
 				
 				//if there are names in this bin add to new list
 				if (newNames != "") {  
@@ -615,6 +644,7 @@ int RemoveGroupsCommand::readName(){
 					//you know you have at least one valid second since first column is valid
 					for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 					out << validSecond[validSecond.size()-1] << endl;
+					uniqueToRedundant[firstCol] = validSecond[0];
 				}
 			}
 			
@@ -709,7 +739,12 @@ int RemoveGroupsCommand::readTax(){
 			if (names.count(name) == 0) {
 				wroteSomething = true;
 				out << name << '\t' << tax << endl;
-			}else {  removedCount++;  }
+			}else {  //if you are not in the accnos file check if you are a name that needs to be changed
+				map<string, string>::iterator it = uniqueToRedundant.find(name);
+				if (it != uniqueToRedundant.end()) {
+					wroteSomething = true;
+					out << it->second << '\t' << tax << endl;
+				}else { removedCount++; }  }
 			
 			m->gobble(in);
 		}