added abundance and sample parameters to get.coremicrobiome command.

[mothur.git] / getcoremicrobiomecommand.h

diff --git a/getcoremicrobiomecommand.h b/getcoremicrobiomecommand.h
new file mode 100644 (file)
index 0000000..c8aaab3
--- /dev/null
+++ b/getcoremicrobiomecommand.h
@@ -0,0 +1,55 @@
+#ifndef Mothur_getcoremicrobiomcommand_h
+#define Mothur_getcoremicrobiomcommand_h
+
+
+//
+//  GetCoreMicroBiomeCommand.h
+//  Mothur
+//
+//  Created by John Westcott on 5/8/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+#include "command.hpp"
+#include "inputdata.h"
+
+/**************************************************************************************************/
+
+class GetCoreMicroBiomeCommand : public Command {
+public:
+    GetCoreMicroBiomeCommand(string);
+    GetCoreMicroBiomeCommand();
+    ~GetCoreMicroBiomeCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "get.coremicrobiome";                  }
+    string getCommandCategory()                { return "OTU-Based Approaches";                } 
+    //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
+    string getHelpString();    
+    string getCitation() { return "http://www.mothur.org/wiki/Get.coremicrobiome"; }
+    string getDescription()            { return "determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances"; }
+    
+    int execute(); 
+    void help() { m->mothurOut(getHelpString()); }     
+    
+private:
+    string relabundfile, sharedfile, inputFileName, format, output;
+    bool allLines;
+    vector<string> Groups;
+    set<string> labels;
+    bool abort;
+    string outputDir;
+    vector<string> outputNames;
+    int samples, abund;
+    
+    int createTable(vector<SharedRAbundFloatVector*>&);
+
+};
+
+/**************************************************************************************************/
+
+
+
+
+#endif