mods to trim.seqs

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 4f4c809e51e7f9308ae4f372bdd2195eb964f6c3..aef789aa7dd80a656a66c3061a2e8cadd1fe081b 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,15 +17,21 @@ 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, taxfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
+               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();
@@ -34,6 +40,8 @@ class GetSeqsCommand : public Command {
                int readAccnos();
                int readList();
                int readTax();
+               int readQual();
+               int compareAccnos();
                
 };