consensus.seqs can now find a consensus on a whole fasta file without needing a listfile

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 809109c486de9f00b39091b863da8a23dfc95a96..b249072e41aba8b7ff0501c1fc946b90c48dfd22 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,22 +17,30 @@ 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();    
                
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
-               bool abort;
+               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               bool abort, dups;
+               map<string, vector<string> > outputTypes;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
-               void readAccnos();
-               void readList();
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readAccnos();
+               int readList();
+               int readTax();
+               int readQual();
                
 };