added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index de48158d9eb7d26adecce2dab1162b32332fec5f..63f83e19a61fec97a6a64121da4f5ea973b5815a 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -572,8 +572,8 @@ int SharedCommand::createMisMatchFile() {
                        
                        m->openOutputFile(outputMisMatchName, outMisMatch);
                        
-                       map<string, string> listNames;
-                       map<string, string>::iterator itList;
+                       set<string> listNames;
+                       set<string>::iterator itList;
                        
                        //go through list and if group returns "not found" output it
                        for (int i = 0; i < SharedList->getNumBins(); i++) {
@@ -581,26 +581,19 @@ int SharedCommand::createMisMatchFile() {
                        
                                string names = SharedList->get(i); 
                                
-                               while (names.find_first_of(',') != -1) { 
-                                       string name = names.substr(0,names.find_first_of(','));
-                                       names = names.substr(names.find_first_of(',')+1, names.length());
+                vector<string> binNames;
+                m->splitAtComma(names, binNames);
+                
+                               for (int j = 0; j < binNames.size(); j++) { 
+                                       string name = binNames[j];
                                        string group = groupMap->getGroup(name);
                                        
                                        if(group == "not found") {      outMisMatch << name << endl;  }
                                        
                                        itList = listNames.find(name);
                                        if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
-                                       else { listNames[name] = name; }
+                                       else { listNames.insert(name); }
                                }
-                       
-                               //get last name
-                               string group = groupMap->getGroup(names);
-                               if(group == "not found") {      outMisMatch << names << endl;  }        
-                               
-                               itList = listNames.find(names);
-                               if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
-                               else { listNames[names] = names; }
-
                        }
                        
                        outMisMatch.close();
@@ -621,9 +614,12 @@ int SharedCommand::createMisMatchFile() {
                                
                                string names = SharedList->get(i); 
                
-                               while (names.find_first_of(',') != -1) { 
-                                       string name = names.substr(0,names.find_first_of(','));
-                                       names = names.substr(names.find_first_of(',')+1, names.length());
+                               vector<string> binNames;
+                m->splitAtComma(names, binNames);
+                
+                               for (int j = 0; j < binNames.size(); j++) { 
+
+                                       string name = binNames[j];
                                        
                                        itList = namesInList.find(name);
                                        if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
@@ -631,12 +627,6 @@ int SharedCommand::createMisMatchFile() {
                                        namesInList[name] = name;
                                        
                                }
-                               
-                               itList = namesInList.find(names);
-                               if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
-
-                               //get last name
-                               namesInList[names] = names;                             
                        }
                        
                        //get names of sequences in groupfile
@@ -674,13 +664,12 @@ int SharedCommand::ListGroupSameSeqs() {
                int error = 0; 
                
                vector<string> groupMapsSeqs = groupMap->getNamesSeqs();
-               
+               
                set<string> groupNamesSeqs;
                for(int i = 0; i < groupMapsSeqs.size(); i++) {
                        groupNamesSeqs.insert(groupMapsSeqs[i]);
                }
                
-               
                //go through list and if group returns "not found" output it
                for (int i = 0; i < SharedList->getNumBins(); i++) {
                        if (m->control_pressed) { return 0; }