sped up the remove.seqs and remove.lineage and get.seqs and get.lineage. fixed bug...

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 1990e9c364d6bdedb257f2801abe55f566de8e29..02cb5d94c2f286f3456f073ccd30db753f4743d3 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -513,24 +513,17 @@ int RemoveSeqsCommand::readName(){
                string name, firstCol, secondCol;
                
                bool wroteSomething = false;
+                               
                
                while(!in.eof()){
                        if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
-
+                       
                        in >> firstCol;         m->gobble(in);          
                        in >> secondCol;                        
-
+                       
                        vector<string> parsedNames;
-                       //parse second column saving each name
-                       while (secondCol.find_first_of(',') != -1) { 
-                               name = secondCol.substr(0,secondCol.find_first_of(','));
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-                               parsedNames.push_back(name);
-                       }
+                       m->splitAtComma(secondCol, parsedNames);
                        
-                       //get name after last ,
-                       parsedNames.push_back(secondCol);
-
                        vector<string> validSecond;  validSecond.clear();
                        for (int i = 0; i < parsedNames.size(); i++) {
                                if (names.count(parsedNames[i]) == 0) {
@@ -541,7 +534,7 @@ int RemoveSeqsCommand::readName(){
                        if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
                                for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
                        }else {
-                                       //if the name in the first column is in the set then print it and any other names in second column also in set
+                               //if the name in the first column is in the set then print it and any other names in second column also in set
                                if (names.count(firstCol) == 0) {
                                        
                                        wroteSomething = true;
@@ -572,10 +565,10 @@ int RemoveSeqsCommand::readName(){
                }
                in.close();
                out.close();
-
+               
                if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
                outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
-                               
+               
                return 0;
        }
        catch(exception& e) {