fixing minor bugs

[mothur.git] / parselistcommand.h

diff --git a/parselistcommand.h b/parselistcommand.h
index bf8ee5daf24a014728b7ed12698ca744d56d1cd6..b3a2f9c71c5a5657c5cef0ccb17c13e43dd673d5 100644 (file)
--- a/parselistcommand.h
+++ b/parselistcommand.h
@@ -14,7 +14,7 @@
 #include "sharedlistvector.h"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 
 
 /* The parselist() command:
@@ -31,13 +31,14 @@ 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;
        SharedListVector* list;
@@ -45,7 +46,8 @@ private:
        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;
 };