X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.h;h=c6671677ff40b0b398cdd4361781c7b9ad0ec1a2;hb=6f9dc7ca71d7b8ed4aba2824f76ae6b29da89f3b;hp=9387bc5954124d00612b5874bb7f084a90ca329d;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/errorchecking.h b/errorchecking.h
index 9387bc5..c667167 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 "validcalculator.h"
+
 
 class ErrorCheck {
 	public:
@@ -26,22 +25,21 @@ class ErrorCheck {
 		GlobalData* globaldata;
 		ValidCommands* validCommand;
 		ValidParameters* validParameter;
-		ValidCalculators* validCalculator;
-		void splitAtDash(string&, vector<string>&);
-		void splitAtDash(string&, set<int>&);
-		void splitAtDash(string&, set<string>&);
 		void validateReadFiles();
 		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, cutoff, format; 
-		string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree;
+		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;
-		vector<string> singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators;
-		
+
+		vector<string> sharedGroups;
 };
 #endif