added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / pcrseqscommand.h

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 45ce6f3f153e6020f00c859b1928cc1d74ea2a55..d35850ce74296fa4f4471927817becd21145dbee 100644 (file)
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -15,6 +15,7 @@
 #include "trimoligos.h"
 #include "alignment.hpp"
 #include "needlemanoverlap.hpp"
+#include "counttable.h"
 
 class PcrSeqsCommand : public Command {
 public:
@@ -25,6 +26,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "pcr.seqs";    }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
        string getDescription()         { return "pcr.seqs"; }
@@ -44,8 +46,8 @@ private:
     vector<linePair> lines;
        bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
     bool abort, keepprimer, keepdots;
-       string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
-       int start, end, pdiffs, processors, length;
+       string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, outputDir, nomatch;
+       int start, end, processors, length;
        
     vector<string> revPrimer, outputNames;
        vector<string> primers;
@@ -54,6 +56,7 @@ private:
     int readName(set<string>&);
     int readGroup(set<string>);
     int readTax(set<string>);
+    int readCount(set<string>);
     bool readOligos();
     bool readEcoli();
        int driverPcr(string, string, string, set<string>&, linePair);