#include "mothur.h"
#include "command.hpp"
-#include "alignment.hpp"
+//#include "alignment.hpp"
#include "classify.h"
//KNN and Bayesian methods modeled from algorithms in
class ClassifySeqsCommand : public Command {
public:
- ClassifySeqsCommand(string);
+ ClassifySeqsCommand(string);
~ClassifySeqsCommand();
int execute();
void help();
};
vector<int> processIDS; //processid
vector<linePair*> lines;
+ vector<string> fastaFileNames;
+ vector<string> namefileNames;
+ map<string, int> nameMap;
+ map<string, int>::iterator itNames;
Classify* classify;
- string fastaFileName, templateFileName, distanceFileName, search, method, taxonomyFileName;
- int processors, kmerSize, numWanted, cutoff;
+ string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir;
+ int processors, kmerSize, numWanted, cutoff, iters;
float match, misMatch, gapOpen, gapExtend;
- bool abort;
+ bool abort, probs;
- int driver(linePair*, string, string);
+ int driver(linePair*, string, string, string);
void appendTaxFiles(string, string);
- void createProcesses(string, string);
+ void createProcesses(string, string, string);
+ string addUnclassifieds(string, int);
};
#endif