#include "command.hpp"
#include "readblast.h"
-#include "sparsematrix.hpp"
#include "nameassignment.hpp"
-#include "globaldata.hpp"
#include "cluster.hpp"
#include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "counttable.h"
/**********************************************************************/
public:
MGClusterCommand(string);
MGClusterCommand();
- ~MGClusterCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~MGClusterCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "mgcluster"; }
+ string getCommandCategory() { return "Clustering"; }
+
+ 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()); }
+
private:
- GlobalData* globaldata;
ReadBlast* read;
NameAssignment* nameMap;
Cluster* cluster;
HCluster* hcluster;
ListVector* list;
+ CountTable* ct;
ListVector oldList;
+ RAbundVector rav;
vector<seqDist> overlapMatrix;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
- 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*&);
};