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

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 6abf06a6fcf11bba1a714c6b3efdfd2be37b7285..305c6e34dd0fcf1a66e434b797ea3a5af991dfd0 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -16,7 +16,12 @@
 class SeqSummaryCommand : public Command {
 public:
        SeqSummaryCommand(string);
+       SeqSummaryCommand();
        ~SeqSummaryCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -24,6 +29,8 @@ private:
        bool abort;
        string fastafile, outputDir;
        int processors;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        struct linePair {
                unsigned long int start;