#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 getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
ReadBlast* read;
NameAssignment* nameMap;
Cluster* cluster;
HCluster* hcluster;
ListVector* list;
ListVector oldList;
- vector<DistNode> overlapMatrix;
- DistNode next;
-
+ vector<seqDist> overlapMatrix;
+ vector<string> outputNames;
- string blastfile, method, namefile, overlapFile, distFile;
+ 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, exitedBreak, merge;
+ bool abort, minWanted, hclusterWanted, merge, hard;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
- vector<DistNode> getSeqs(ifstream&);
+ vector<seqDist> getSeqs(ifstream&);
};