working on testing

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 22847dce9b45604515c97fab55a2673813324ec2..6ea7305265a6725a6a6290f6de028b307c5e8a0b 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -9,12 +9,14 @@
  *
  */
 
+/* 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 "readotu.h"
 #include "fastamap.h"
+#include "groupmap.h"
 
 
 class GlobalData;
@@ -22,21 +24,27 @@ class GlobalData;
 class BinSeqCommand : public Command {
        
 public:
-       BinSeqCommand();        
+       BinSeqCommand(string);  
        ~BinSeqCommand();
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
        ListVector* list;
-       ReadMatrix* read;
+       ReadOTUFile* 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, namesfile, groupfile, label, outputDir;
        ofstream out;
        ifstream in, inNames;
+       vector<string> outputNames;
        
        void readNamesFile();
+       int process(ListVector*);
 };
 
 #endif