added get.metacommunity command.

[mothur.git] / getmetacommunitycommand.h

diff --git a/getmetacommunitycommand.h b/getmetacommunitycommand.h
new file mode 100644 (file)
index 0000000..62070d6
--- /dev/null
+++ b/getmetacommunitycommand.h
@@ -0,0 +1,64 @@
+//
+//  getmetacommunitycommand.h
+//  Mothur
+//
+//  Created by SarahsWork on 4/9/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_getmetacommunitycommand_h
+#define Mothur_getmetacommunitycommand_h
+
+#include "command.hpp"
+#include "inputdata.h"
+
+/**************************************************************************************************/
+
+class GetMetaCommunityCommand : public Command {
+public:
+    GetMetaCommunityCommand(string);
+    GetMetaCommunityCommand();
+    ~GetMetaCommunityCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "get.metacommunity";           }
+    string getCommandCategory()                { return "OTU-Based Approaches";         }
+    
+    string getOutputPattern(string);
+    
+       string getHelpString();
+    string getCitation() { return "http://www.mothur.org/wiki/Get.metacommunity"; }
+    string getDescription()            { return "brief description"; }
+    
+    int execute();
+    void help() { m->mothurOut(getHelpString()); }
+    
+private:
+    bool abort, allLines;
+    string outputDir;
+    vector<string> outputNames;
+    string sharedfile;
+    int minpartitions, maxpartitions, optimizegap;
+    vector<string> Groups;
+    set<string> labels;
+    
+    int process(vector<SharedRAbundVector*>&);
+    vector<double> generateDesignFile(int, string);
+    int generateSummaryFile(int, string, string, string, string);
+
+};
+
+/**************************************************************************************************/
+struct summaryData {
+    
+    string name;
+    double refMean, difference;
+    vector<double> partMean, partLCI, partUCI;
+    
+};
+/**************************************************************************************************/
+
+
+
+
+#endif