X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=e5a3bb2edc7fc97dacb89393ef3a2968b64247b4;hb=1b0bddfbf4ac5df7e2dad03c8a5350e71b052f78;hp=252a92573d036c47f4d45235113adef1fc44727a;hpb=8742edef7a51b82834289e570d336f5a81ba1f2b;p=mothur.git

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 252a925..e5a3bb2 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -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 = "";  }
@@ -204,7 +209,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -273,7 +278,8 @@ int RemoveGroupsCommand::execute(){
 			//make sure groups are valid
 			//takes care of user setting groupNames that are invalid or setting groups=all
 			SharedUtil* util = new SharedUtil();
-			util->setGroups(Groups, groupMap->namesOfGroups);
+			vector<string> namesGroups = groupMap->getNamesOfGroups();
+			util->setGroups(Groups, namesGroups);
 			delete util;
 			
 			//fill names with names of sequences that are from the groups we want to remove 
@@ -369,9 +375,16 @@ 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);
 		}
@@ -403,23 +416,23 @@ int RemoveGroupsCommand::readShared(){
 		vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
 	
 		//save m->Groups
-		vector<string> allGroupsNames = m->namesOfGroups;
-		vector<string> mothurOutGroups = m->Groups;
+		vector<string> allGroupsNames = m->getAllGroups();
+		vector<string> mothurOutGroups = m->getGroups();
 		
 		vector<string> groupsToKeep;
 		for (int i = 0; i < allGroupsNames.size(); i++) {
-			if (!m->inUsersGroups(allGroupsNames[i], m->Groups)) {
+			if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
 				groupsToKeep.push_back(allGroupsNames[i]);
 			}
 		}
 		
-		if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->Groups = mothurOutGroups; delete tempInput; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
+		if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
 		
 		//reset read 
 		for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 		delete tempInput;
-		m->Groups = groupsToKeep;
-		m->namesOfGroups.clear();
+		m->setGroups(groupsToKeep);
+		m->clearAllGroups();
 		m->names.clear();
 		m->saveNextLabel = "";
 		m->printedHeaders = false;
@@ -458,7 +471,7 @@ int RemoveGroupsCommand::readShared(){
 		}
 		
 		
-		m->Groups = mothurOutGroups;
+		m->setGroups(mothurOutGroups);
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine();  }
 		
@@ -517,12 +530,23 @@ 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 != "") {  
@@ -614,6 +638,7 @@ 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];
 				}
 			}
 			
@@ -708,7 +733,12 @@ 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);
 		}
@@ -745,7 +775,7 @@ void RemoveGroupsCommand::readAccnos(){
 		}
 		in.close();	
 		
-		m->Groups = Groups;
+		m->setGroups(Groups);
 		
 	}
 	catch(exception& e) {