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

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 9d8e7960f5c2e949f021602aaf1aa36e7d3e82e0..ea93b5a1c4e0427cc43157a5d77f995bb3f2308b 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,7 +17,12 @@ class GetSeqsCommand : public Command {
        public:
        
                GetSeqsCommand(string);
+               GetSeqsCommand();
                ~GetSeqsCommand(){};
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
@@ -25,7 +30,8 @@ class GetSeqsCommand : public Command {
                set<string> names;
                vector<string> outputNames;
                string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
-               bool abort;
+               bool abort, dups;
+               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();