added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index cb715ce05bc1edad8f2790cd78b67a356eafd7c3..cc904ec7f246aed91970b41cf52e39b7d32b896b 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "referencedb.h"
 
 struct Compare {
        int AA, AT, AG, AC,     TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
@@ -50,17 +51,20 @@ public:
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+       string getDescription()         { return "seq.error"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
        bool abort;
+       ReferenceDB* rdb;
        
        struct linePair {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
        
        vector<int> processIDS;   //processid
@@ -78,13 +82,13 @@ private:
        void printErrorQuality(map<char, vector<int> >);
        void printQualityFR(vector<vector<int> >, vector<vector<int> >);
        
-       int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
+       int setLines(string, string, string, vector<unsigned long long>&, vector<unsigned long long>&, vector<unsigned long long>&);
        int driver(string, string, string, string, string, string, linePair, linePair, linePair);
        int createProcesses(string, string, string, string, string, string);
 
        string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
        double threshold;
-       bool ignoreChimeras, filter;
+       bool ignoreChimeras, save;
        int numRefs, processors;
        int maxLength, totalBases, totalMatches;
        //ofstream errorSummaryFile, errorSeqFile;