X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistcommand.h;h=9e9e968077bc4394b6c82f60bef91b18fe19ca1b;hb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;hp=73c1070a7ca371cbbea5aa7495814c49146b5d82;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/parselistcommand.h b/parselistcommand.h
index 73c1070..9e9e968 100644
--- a/parselistcommand.h
+++ b/parselistcommand.h
@@ -9,16 +9,12 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#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:
@@ -35,22 +31,24 @@ 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;
 };
 
-#endif
\ No newline at end of file
+#endif