#include "readblast.h"
#include "sparsematrix.hpp"
#include "nameassignment.hpp"
-#include "globaldata.hpp"
#include "cluster.hpp"
#include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
/**********************************************************************/
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;
HCluster* hcluster;
ListVector* list;
ListVector oldList;
+ RAbundVector rav;
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, large;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);
+ void createRabund(map<string, int>);
};