added logfile feature

[mothur.git] / parselistcommand.h

diff --git a/parselistcommand.h b/parselistcommand.h
index 4358762df8da87ad8474e65940c85ed002b52be9..9e9e968077bc4394b6c82f60bef91b18fe19ca1b 100644 (file)
--- a/parselistcommand.h
+++ b/parselistcommand.h
@@ -9,15 +9,12 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <map>
 #include "command.hpp"
 #include "rabundvector.hpp"
 #include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 
 
 /* The parselist() command:
@@ -34,21 +31,23 @@ class ParseListCommand : public Command {
 public:
        ParseListCommand();     
        ~ParseListCommand();
-       int execute();  
+       int execute();
+       void help() {}  
        
 private:
        GlobalData* globaldata;
        GroupMap* groupMap;
        InputData* input;
-       ReadMatrix* read;
+       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;
 };