added alignment code

[mothur.git] / errorchecking.h

diff --git a/errorchecking.h b/errorchecking.h
index 50cc00511a08fa71754d2dbf51fd76406d2925ea..d6388f7d2337bacafd148a201cc62a27f83e1375 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:
@@ -26,23 +26,20 @@ class ErrorCheck {
                ValidCommands* validCommand;
                ValidParameters* validParameter;
                void validateReadFiles();
-       //      bool validCommandParameter(string, string);
-       //      bool validParameterValue(string, string);
                void validateReadDist();
                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;
+               string templatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
                string commandName, optionText;
                bool errorFree;
 
                vector<string> sharedGroups;
-       //      map <string, vector<string> > commandParameters;
-       ///     map <string, vector<double> > intParams;
-       //      double piSent;
-
 };
 #endif