#include "mothur.h"
#include "command.hpp"
-//#include "alignment.hpp"
#include "classify.h"
//KNN and Bayesian methods modeled from algorithms in
public:
ClassifySeqsCommand(string);
+ ClassifySeqsCommand();
~ClassifySeqsCommand();
+
+ vector<string> setParameters();
+ string getCommandName() { return "classify.seqs"; }
+ string getCommandCategory() { return "Phylotype Analysis"; }
+ string getHelpString();
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
struct linePair {
- int start;
- int numSeqs;
- linePair(int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
+
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<string> fastaFileNames;
vector<string> namefileNames;
- map<string, int> nameMap;
- map<string, int>::iterator itNames;
+ vector<string> groupfileNames;
+ vector<string> outputNames;
+ map<string, vector<string> > nameMap;
+ map<string, vector<string> >::iterator itNames;
Classify* classify;
int driver(linePair*, string, string, string);
void appendTaxFiles(string, string);
- void createProcesses(string, string, string);
+ int createProcesses(string, string, string);
string addUnclassifieds(string, int);
int MPIReadNamesFile(string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
};