added modify names parameter to set.dir

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index df7ea7593dd266c71a3a1b7a49c03c70596a368f..c93041f348505d7482e9a18d2658d29919eae309 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -14,12 +14,9 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readotu.h"
 #include "fastamap.h"
 #include "groupmap.h"
-
-
-class GlobalData;
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
        
@@ -27,27 +24,31 @@ public:
        BinSeqCommand(string);  
        BinSeqCommand();
        ~BinSeqCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "bin.seqs";                    }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
+       string getDescription()         { return "maps sequences to otus"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
        
 private:
-       GlobalData* globaldata;
+       CountTable ct;
        ListVector* list;
-       ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string filename, fastafile, namesfile, groupfile, label, outputDir;
+       string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
        ofstream out;
        ifstream in, inNames;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        void readNamesFile();
        int process(ListVector*);