added pipeline commands which involved change to command factory and command class...

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 617f5ec7ac98f17f358c383ca424ebd817cb3227..df7ea7593dd266c71a3a1b7a49c03c70596a368f 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -16,6 +16,7 @@
 #include "listvector.hpp"
 #include "readotu.h"
 #include "fastamap.h"
+#include "groupmap.h"
 
 
 class GlobalData;
@@ -23,9 +24,15 @@ class GlobalData;
 class BinSeqCommand : public Command {
        
 public:
-       BinSeqCommand();        
+       BinSeqCommand(string);  
+       BinSeqCommand();
        ~BinSeqCommand();
-       int execute();  
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -33,11 +40,17 @@ private:
        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;
+       map<string, vector<string> > outputTypes;
        
        void readNamesFile();
+       int process(ListVector*);
 };
 
 #endif