added modify names parameter to set.dir

[mothur.git] / pipelinepdscommand.h

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index 8a8a195eef38c9787332c2b029c889f693c55639..22386bcc697c2e3c64767ad99dd9fafaaa5d206f 100644 (file)
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -20,20 +20,25 @@ class PipelineCommand : public Command {
        
 public:
        PipelineCommand(string);
-       PipelineCommand() {}
-       ~PipelineCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; } //empty
-       int execute();
-       void help();
+       PipelineCommand() { abort = true; calledHelp = true; setParameters(); }
+       ~PipelineCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pipeline.pds";        }
+       string getCommandCategory()             { return "Hidden";                      }
+       string getHelpString(); 
+    string getOutputPattern(string) { return ""; }     
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Pipeline.pds"; }
+       string getDescription()         { return "pat's pipeline"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        bool abort;
        CommandFactory* cFactory;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        vector<string> commands;
        string outputDir, sffFile, alignFile, oligosFile, taxonomyFile, pipeFilename, classifyFile, chimeraFile;
        int processors;
@@ -43,7 +48,7 @@ private:
        void createPatsPipeline();
        bool parseCommand(string, string&, string&);
        bool checkForValidAndRequiredParameters(string, string, map<string, vector<string> >&);
-       bool fillInMothurMade(string&, map<string, vector<string> >);
+       bool fillInMothurMade(string&, map<string, vector<string> >&);
 };
 
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