fixing minor bugs

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 7bd1ead9dfa9e6cd62d051aa337697350703d9c3..e07dadc1713989455a7fa1f35b6cdaa6767abf6c 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -10,7 +10,7 @@
  */
 
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "sharedcommand.h"
@@ -33,18 +33,24 @@ class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-       ReadOtuCommand();
+       ReadOtuCommand(string);
        ~ReadOtuCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       //ReadOTUFile* read;
        InputData* input;
        Command* shared;
        Command* parselist;
        GroupMap* groupMap;
-       string filename;
+       string filename, listfile, orderfile, sharedfile, line, label, groupfile, sabundfile, rabundfile, format;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+
 };
 
 #endif