modified read.otu and shared command

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index f00369ba8f4116db8d8e5dee015f60fa52f2a432..6ec35412c3c82206bef933787c820ca36e2158d2 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,14 +9,11 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "sharedcommand.h"
-#include "parselistcommand.h"
 
 /* The read.otu must be run before you execute a collect.single, rarefaction.single, summary.single, 
 collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund 
@@ -35,18 +32,23 @@ 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