added reverse.seqs command

[mothur.git] / errorchecking.h

diff --git a/errorchecking.h b/errorchecking.h
index 1b023e079cf8ab15c8539596dc72841be7edf7a3..7f9e4580bd8b37110c241d438543916ef9f3b9c2 100644 (file)
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -9,12 +9,11 @@
  *
  */
 
-#include <iostream>
-#include <map>
+#include "mothur.h"
 #include "globaldata.hpp"
 #include "validcommands.h"
 #include "validparameter.h"
-#include "utilities.hpp"
+
 
 class ErrorCheck {
        public:
@@ -31,12 +30,15 @@ class ErrorCheck {
                void validateReadPhil();
                void validateParseFiles();
                void validateTreeFiles();
+               void validateBinFiles();
                void clear();
                void refresh();
                string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, cutoff, format; 
-               string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree;
+               string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, countends, processors, size;
+               string candidatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
                string commandName, optionText;
                bool errorFree;
-               
+
+               vector<string> sharedGroups;
 };
 #endif