#include "mothur.h"
#include "command.hpp"
-#include "alignment.hpp"
+//#include "alignment.hpp"
#include "classify.h"
+//KNN and Bayesian methods modeled from algorithms in
+//Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences
+//into the New Bacterial Taxonomy†
+//Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1*
+//Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University,
+//East Lansing, Michigan 48824
+//Received 10 January 2007/Accepted 18 June 2007
+
+
+
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;
+ 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);
+ int driver(linePair*, string, string, string);
void appendTaxFiles(string, string);
- void createProcesses(string);
+ void createProcesses(string, string, string);
+ string addUnclassifieds(string, int);
};
#endif