changes to trim.flows command

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index a183151f3580ab5232a1108c25a58c22a0c540e6..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();    
        
@@ -38,9 +43,11 @@ private:
        GroupMap* groupMap;
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string filename, fastafile, namesfile, groupfile, 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*);