changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 972f30e8e0e008111d14bc49670dc926a98d360f..beb2f4bcbfe31ed89bdb2f9c393585a4ffae3667 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -9,30 +9,32 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "inputdata.h"
-
-/* The read.otu command parameter options are listfile, sabundfile, rabundfile and orderfile.  
-The read.otu command should be in the following format: 
-read.otu(listfile=yourListFile, orderfile=yourOrderFile). The listfile, sabundfile or rabundfile are required, but only one may be used. */
+#include "groupmap.h"
+#include "sharedcommand.h"
 
 class GlobalData;
 
 class ReadOtuCommand : public Command {
 public:
-       ReadOtuCommand();
+       ReadOtuCommand(string);
        ~ReadOtuCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
        InputData* input;
-       string filename;
+       Command* shared;
+       GroupMap* groupMap;
+       string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir;
+       vector<string> Groups;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+
 };
 
-#endif
\ No newline at end of file
+#endif