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 aceba65da17315de31515750a62fc53f4b7b9a48..df7ea7593dd266c71a3a1b7a49c03c70596a368f 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -25,7 +25,12 @@ class BinSeqCommand : public Command {
        
 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();    
        
@@ -36,18 +41,16 @@ private:
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
        bool abort, allLines;
-       set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
-       string filename, fastafile, namesfile, groupfile, line, label;
+       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*, int);
+       int process(ListVector*);
 };
 
 #endif