#include "command.hpp"
#include "readblast.h"
-#include "sparsematrix.hpp"
#include "nameassignment.hpp"
#include "cluster.hpp"
#include "hcluster.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
+#include "counttable.h"
/**********************************************************************/
vector<string> setParameters();
string getCommandName() { return "mgcluster"; }
string getCommandCategory() { return "Clustering"; }
- string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Mgcluster"; }
+ string getHelpString();
+ string getOutputPattern(string);
+ 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()); }
Cluster* cluster;
HCluster* hcluster;
ListVector* list;
+ CountTable* ct;
ListVector oldList;
+ RAbundVector rav;
vector<seqDist> overlapMatrix;
vector<string> outputNames;
- string blastfile, method, namefile, overlapFile, distFile, outputDir;
+ string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
ofstream sabundFile, rabundFile, listFile;
double cutoff;
float penalty;
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);
+ void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};