added logfile feature

[mothur.git] / parselistcommand.h

diff --git a/parselistcommand.h b/parselistcommand.h
index 0477acdb06e26ada0f64a25370138a75dc7a06ff..9e9e968077bc4394b6c82f60bef91b18fe19ca1b 100644 (file)
--- a/parselistcommand.h
+++ b/parselistcommand.h
@@ -31,7 +31,8 @@ class ParseListCommand : public Command {
 public:
        ParseListCommand();     
        ~ParseListCommand();
-       int execute();  
+       int execute();
+       void help() {}  
        
 private:
        GlobalData* globaldata;
@@ -39,13 +40,14 @@ private:
        InputData* input;
        ReadOTUFile* read;
        map<string, ofstream*> filehandles;
-       map<string, SharedListVector*> groupOfLists;
+       map<string, SharedListVector*> mapOfLists;
        SharedListVector* list;
        map<string, string> listGroups; //maps group name to sequences from that group in a specific OTU
        map<string, string>::iterator it;
        map<string, SharedListVector*>::iterator it2;
        map<string, ofstream*>::iterator it3;
-       void parse(int);
+       void parse(int, SharedListVector*);
+       void process(SharedListVector*);
        string fileroot;
 };