updated errorchecking so it checks if the parameter is valid for the command.

[mothur.git] / errorchecking.h

diff --git a/errorchecking.h b/errorchecking.h
index 9387bc5954124d00612b5874bb7f084a90ca329d..4c9fe8615c0819f0ec6dfad5b743d737ee365e4e 100644 (file)
--- 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"
+#include "utilities.hpp"
 
 class ErrorCheck {
        public:
@@ -26,10 +25,6 @@ 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();
@@ -37,11 +32,11 @@ class ErrorCheck {
                void validateTreeFiles();
                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, treefile, sharedfile, cutoff, format; 
+               string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund;
                string commandName, optionText;
                bool errorFree;
-               vector<string> singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators;
-               
+
+               vector<string> sharedGroups;
 };
 #endif