X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.h;h=ac09f6ed49bdb074bbe2c6acfd404fef77cc7116;hb=dc874a77f24b3808775e2ce7e39595c647a07f82;hp=8b3c0cafb0e6b787d5d408083828ab39757420bc;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/errorchecking.h b/errorchecking.h
index 8b3c0ca..ac09f6e 100644
--- 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:
@@ -27,23 +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, countends, processors, size;
+		string candidatefile, 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