changed defaults for filter.seqs()

[mothur.git] / errorchecking.h

diff --git a/errorchecking.h b/errorchecking.h
index 4c9fe8615c0819f0ec6dfad5b743d737ee365e4e..c6671677ff40b0b398cdd4361781c7b9ad0ec1a2 100644 (file)
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -13,7 +13,7 @@
 #include "globaldata.hpp"
 #include "validcommands.h"
 #include "validparameter.h"
-#include "utilities.hpp"
+
 
 class ErrorCheck {
        public:
@@ -30,10 +30,13 @@ class ErrorCheck {
                void validateReadPhil();
                void validateParseFiles();
                void validateTreeFiles();
+               void validateBinFiles();
+               void validateSeqsFiles();
                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, abund;
+               string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, cutoff, format; 
+               string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, ends, processors, size;
+               string candidatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
                string commandName, optionText;
                bool errorFree;