added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index a1dac221b891a8551a36b7493d5bb7a603204cf5..ea2c1de8603d746277017d8b557fcc5171c9af39 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 +25,22 @@ 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 getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
+       string getDescription()         { return "cluster your sequences into OTUs using a blast file"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
        ReadBlast* read;
        NameAssignment* nameMap;
        Cluster* cluster;
@@ -37,13 +48,14 @@ private:
        ListVector* list;
        ListVector oldList;
        vector<seqDist> overlapMatrix;
+       vector<string> outputNames;
        
        string blastfile, method, namefile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
        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);