changed defaults in allign.seqs command

[mothur.git] / errorchecking.h

diff --git a/errorchecking.h b/errorchecking.h
index d1e2f82451cc3f5d5e4be6d7496894d6b884e9cc..c6671677ff40b0b398cdd4361781c7b9ad0ec1a2 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"
+
 
 class ErrorCheck {
        public:
@@ -26,21 +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();
-               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;
+               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 candidatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
                string commandName, optionText;
                bool errorFree;
-               vector<string> singleEsimators, sharedEstimators, rareEstimators, summaryEstimators, sharedRareEstimators;
-               
+
+               vector<string> sharedGroups;
 };
 #endif