finished shhh.seqs command, fixed bug with remove.groups and get.groups that caused...

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index e8f42dda532fab7f252de8c95e220c8eb27fa8f8..e533bc47defa9467b345a0a58cc8b80b59710275 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -384,6 +384,15 @@ 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);
@@ -499,10 +508,26 @@ 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 != "") {  
@@ -594,6 +619,7 @@ 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];
                                }
                        }
                        
@@ -687,6 +713,13 @@ 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);