X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.h;h=03e6826d1276b4efbdf12b5fce0aeb4cdea8fb08;hb=a3d9877d9c62058dbe167ceca159f4b76744f1cf;hp=2c6390c1083e0ca72836f7c21c3f8c438a5c362e;hpb=f27b66ce6415eb14c434f9850019c7cf140e023e;p=mothur.git

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 2c6390c..03e6826 100644
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,7 +12,7 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "alignment.hpp"
+//#include "alignment.hpp"
 #include "classify.h"
 
 //KNN and Bayesian methods modeled from algorithms in
@@ -28,30 +28,41 @@
 class ClassifySeqsCommand : public Command {
 	
 public:
-	ClassifySeqsCommand(string);	
+	ClassifySeqsCommand(string);
 	~ClassifySeqsCommand();
 	int execute(); 
 	void help();	
 	
 private:
 	struct linePair {
-		int start;
+		unsigned long int start;
 		int numSeqs;
-		linePair(int i, int j) : start(i), numSeqs(j) {}
+		linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
 	};
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
+	vector<string> fastaFileNames;
+	vector<string> namefileNames;
+	vector<string> groupfileNames;
+	map<string, vector<string> > nameMap;
+	map<string,  vector<string> >::iterator itNames;
 	
 	Classify* classify;
 	
-	string fastaFileName, templateFileName, distanceFileName, search, method, taxonomyFileName;
+	string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
 	int processors, kmerSize, numWanted, cutoff, iters;
 	float match, misMatch, gapOpen, gapExtend;
 	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);
+	
+	int MPIReadNamesFile(string);
+	#ifdef USE_MPI
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	#endif
 };
 
 #endif