changed rarefaction.single output

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 5021f4085534cfc84a17d5875e449cf90f9f1d53..0c42b7dad8281b1d9edd49550c3df95ae773c7e8 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -189,6 +189,11 @@ GetGroupsCommand::GetGroupsCommand(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") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
@@ -375,6 +380,15 @@ int GetGroupsCommand::readFasta(){
                                        
                                        currSeq.printSequence(out);
                                        selectedCount++;
+                               }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);
+                                               selectedCount++;
+                                       }
                                }
                        }
                        m->gobble(in);
@@ -490,10 +504,26 @@ int GetGroupsCommand::readList(){
                                        
                                        //if that name is in the .accnos file, add it
                                        if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++;  }
+                                       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 + ",";
+                                                       selectedCount++;
+                                               }
+                                       }
                                }
                                
                                //get last name
                                if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  }
+                               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 + ",";
+                                               selectedCount++;
+                                       }
+                               }
                                
                                //if there are names in this bin add to new list
                                if (newNames != "") {  
@@ -585,6 +615,7 @@ int GetGroupsCommand::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];
                                }
                        }
                        
@@ -678,6 +709,13 @@ int GetGroupsCommand::readTax(){
                        if (names.count(name) != 0) {
                                wroteSomething = true;
                                out << name << '\t' << tax << endl;
+                       }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;
+                               }
                        }
                        
                        m->gobble(in);