working on kendall

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index e2ff648283a9c00569a8d2a4170a040b4a494902..df7ea7593dd266c71a3a1b7a49c03c70596a368f 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -24,9 +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;
@@ -35,11 +41,16 @@ private:
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, namesfile, groupfile;
+       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