added citation function to commands

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 89b72fceb2ad6c57cf0cde5ae531bf985bf3468f..d5c784e27a28bb27e6b7cbdadbb8b94e25b199b5 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -14,9 +14,10 @@
 #include "readblast.h"
 #include "sparsematrix.hpp"
 #include "nameassignment.hpp"
-#include "globaldata.hpp"
 #include "cluster.hpp"
 #include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
 
 /**********************************************************************/
 
@@ -24,12 +25,20 @@ class MGClusterCommand : public Command {
 
 public:
        MGClusterCommand(string);
-       ~MGClusterCommand();
-       int execute();
-       void help();
+       MGClusterCommand();
+       ~MGClusterCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "mgcluster";   }
+       string getCommandCategory()             { return "Clustering";  }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Mgcluster"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        ReadBlast* read;
        NameAssignment* nameMap;
        Cluster* cluster;
@@ -37,12 +46,14 @@ private:
        ListVector* list;
        ListVector oldList;
        vector<seqDist> overlapMatrix;
+       vector<string> outputNames;
        
        string blastfile, method, namefile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
-       float cutoff, penalty;
+       double cutoff;
+       float penalty;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge;
+       bool abort, minWanted, hclusterWanted, merge, hard;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);