added group option to trim.seqs so you can provide your own groupfile instead of...

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index b533f2864eb44e9091f1eacaaeab35fabbf00e01..7cf357e07499ad5797dec8bbc1e647c163993aa8 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -60,7 +60,12 @@ class SffInfoCommand : public Command {
        
 public:
        SffInfoCommand(string);
+       SffInfoCommand();
        ~SffInfoCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -69,6 +74,7 @@ private:
        vector<string> filenames, outputNames, accnosFileNames;
        bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
        set<string> seqNames;
+       map<string, vector<string> > outputTypes;
        
        int extractSffInfo(string, string);
        int readCommonHeader(ifstream&, CommonHeader&);
@@ -77,7 +83,7 @@ private:
        
        int printCommonHeader(ofstream&, CommonHeader&); 
        int printHeader(ofstream&, Header&);
-       int printSffTxtSeqData(ofstream&, seqRead&);
+       int printSffTxtSeqData(ofstream&, seqRead&, Header&);
        int printFlowSeqData(ofstream&, seqRead&, Header&);
        int printFastaSeqData(ofstream&, seqRead&, Header&);
        int printQualSeqData(ofstream&, seqRead&, Header&);