working on pam

[mothur.git] / deuniqueseqscommand.h

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
index 96ed29bd6aaa0f5a717d5164aa7a5a3e538dbaaf..042ff498fce19a60cd51d7b1393ec2cd4074123c 100644 (file)
--- a/deuniqueseqscommand.h
+++ b/deuniqueseqscommand.h
@@ -23,7 +23,12 @@ public:
        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()); }  
@@ -31,13 +36,10 @@ public:
        
 private:
 
-       string fastaFile, nameFile, outputDir;
+       string fastaFile, nameFile, outputDir, countfile;
        vector<string> outputNames;
        bool abort;
-       
-       map<string, string> nameMap;
-       
-       int readNamesFile();
+
        
 };