]> git.donarmstrong.com Git - mothur.git/blobdiff - pipelinepdscommand.h
removed read.dist, read.otu, read.tree and globaldata. added current to defaults...
[mothur.git] / pipelinepdscommand.h
index 289a909c9d6eef64f4ad2fe61d136592c51120b6..13695a6ec9a178918ab74242d9a2f05a89b9ead7 100644 (file)
@@ -20,20 +20,21 @@ class PipelineCommand : public Command {
        
 public:
        PipelineCommand(string);
-       PipelineCommand() { abort = true; calledHelp = true; }
-       ~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(); 
+       
+       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;