changed rarefaction.single output

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 252a92573d036c47f4d45235113adef1fc44727a..e5a3bb2edc7fc97dacb89393ef3a2968b64247b4 100644 (file)
--- 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) {