added name option to trim.seqs

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 0fdf6fce6647269d476945031255bb585e78ba83..abfaa4b8a088713278a9384c08909f9eaaad70d2 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -64,13 +64,16 @@ 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();
+       ~SffInfoCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "sffinfo";                                     }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        string sffFilename, sfftxtFilename, outputDir, accnosName;
@@ -78,7 +81,6 @@ private:
        bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
        int mycount;
        set<string> seqNames;
-       map<string, vector<string> > outputTypes;
        
        //extract sff file functions
        int extractSffInfo(string, string);