added command descriptions

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 24c29a107b8189778c62b2eeb49258957a321be6..c0d368770cfa8df11560d2b89fee200231cb0dc3 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -17,20 +17,22 @@ class SeqSummaryCommand : public Command {
 public:
        SeqSummaryCommand(string);
        SeqSummaryCommand();
-       ~SeqSummaryCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SeqSummaryCommand(){}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+       string getDescription()         { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
        bool abort;
        string fastafile, outputDir, namefile;
        int processors;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        map<string, int> nameMap;
        
        struct linePair {