changes while testing

[mothur.git] / deuniqueseqscommand.h

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
index 13176a80a413a1bce9d84bb4cf496702a554c446..a6d467a16a96c56ca3f1282d7c7fbbdfbdf02ca7 100644 (file)
--- a/deuniqueseqscommand.h
+++ b/deuniqueseqscommand.h
@@ -19,18 +19,25 @@ public:
        DeUniqueSeqsCommand(string);
        DeUniqueSeqsCommand();
        ~DeUniqueSeqsCommand() {}
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "deunique.seqs";               }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
+       string getDescription()         { return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
 
        string fastaFile, nameFile, outputDir;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        bool abort;
        
        map<string, string> nameMap;