added modify names parameter to set.dir

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 1fb5664b0c018c4120881055014ec08a4e6d5559..c93041f348505d7482e9a18d2658d29919eae309 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -16,6 +16,7 @@
 #include "listvector.hpp"
 #include "fastamap.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
        
@@ -27,8 +28,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "bin.seqs";                    }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
        string getDescription()         { return "maps sequences to otus"; }
        
@@ -36,14 +38,14 @@ public:
        void help() { m->mothurOut(getHelpString()); }          
        
 private:
-       
+       CountTable ct;
        ListVector* list;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
+       string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
        ofstream out;
        ifstream in, inNames;
        vector<string> outputNames;