added modify names parameter to set.dir

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 22847dce9b45604515c97fab55a2673813324ec2..c93041f348505d7482e9a18d2658d29919eae309 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -9,34 +9,49 @@
  *
  */
 
+/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
 
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readmatrix.hpp"
 #include "fastamap.h"
-
-
-class GlobalData;
+#include "groupmap.h"
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
        
 public:
-       BinSeqCommand();        
+       BinSeqCommand(string);  
+       BinSeqCommand();
        ~BinSeqCommand();
-       int execute();  
+       
+       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;
-       ReadMatrix* read;
        InputData* input;
        FastaMap* fasta;
-       string filename, fastafile, namesfile;
+       GroupMap* groupMap;
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
        ofstream out;
        ifstream in, inNames;
+       vector<string> outputNames;
        
        void readNamesFile();
+       int process(ListVector*);
 };
 
 #endif