X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.h;h=16549135aacbe25e36d89f21c503f1baae2fe659;hb=002421a439168e2610a2b62f1318f21c7202fe6d;hp=a73aa0c576f1dc6a3437d9c37557aa89cc0b451c;hpb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63;p=mothur.git

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index a73aa0c..1654913 100644
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,36 +12,65 @@
 
 #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();
 	~ClassifySeqsCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute(); 
 	void help();	
 	
 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;
+	vector<string> groupfileNames;
+	vector<string> outputNames;
+	map<string, vector<string> > nameMap;
+	map<string,  vector<string> >::iterator itNames;
+	map<string, vector<string> > outputTypes;
 	
 	Classify* classify;
 	
-	string fastaFileName, templateFileName, distanceFileName, search, method, taxonomyFileName;
-	int processors, kmerSize, numWanted, cutoff;
+	string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
+	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); 
+	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<unsigned long int>&);
+	#endif
 };
 
 #endif