X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.h;h=5057ab02b2962d92ea3814fdfabf5e039eda2dd7;hb=37a2c0b7dc68bfa53c8f38a713259929c4c46a9f;hp=55795b2d97cdfb3c194ccf5d27a2dc1d1bd65e3b;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/errorchecking.h b/errorchecking.h
index 55795b2..5057ab0 100644
--- a/errorchecking.h
+++ b/errorchecking.h
@@ -9,13 +9,11 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <map>
+#include "mothur.h"
 #include "globaldata.hpp"
 #include "validcommands.h"
 #include "validparameter.h"
-#include "validcalculator.h"
+
 
 class ErrorCheck {
 	public:
@@ -27,20 +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(string);
-		void validateParseFiles(string);
+		void validateReadPhil();
+		void validateParseFiles();
+		void validateTreeFiles();
+		void validateBinFiles();
+		void validateSeqsFiles();
 		void clear();
-		string distfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, cutoff, format; 
-		string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary;
+		void refresh();
+		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 templatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
 		string commandName, optionText;
 		bool errorFree;
-		vector<string> singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators;
-		
+
+		vector<string> sharedGroups;
 };
-#endif
\ No newline at end of file
+#endif