added command descriptions

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index b8ab242e187b2f1b0fccc8b087e7c17f2cc0c903..3642295b54af9d46fd246ad642065952af7295ab 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -23,7 +23,9 @@ public:
        string getCommandName()                 { return "screen.seqs";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
        string getHelpString(); 
-       
+       string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
+       string getDescription()         { return "enables you to keep sequences that fulfill certain user defined criteria"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -42,6 +44,7 @@ private:
        int screenNameGroupFile(set<string>);
        int screenGroupFile(set<string>);
        int screenAlignReport(set<string>);
+       int screenQual(set<string>);
        
        int driver(linePair*, string, string, string, set<string>&);
        int createProcesses(string, string, string, set<string>&);
@@ -51,7 +54,7 @@ private:
        #endif
 
        bool abort;
-       string fastafile, namefile, groupfile, alignreport, outputDir;
+       string fastafile, namefile, groupfile, alignreport, outputDir, qualfile;
        int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
        vector<string> outputNames;
        vector<string> optimize;