X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.h;h=639ae6543082a7162b270da16137078da5c8e362;hb=5c80ce8b80938d41cf6c64a017fa6fd50d45de5b;hp=2223593c4e7758ac48844dbf7d5093b20f361b5d;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 2223593..639ae65 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
@@ -28,7 +28,7 @@
 class ClassifySeqsCommand : public Command {
 	
 public:
-	ClassifySeqsCommand(string);	
+	ClassifySeqsCommand(string);
 	~ClassifySeqsCommand();
 	int execute(); 
 	void help();	
@@ -43,12 +43,13 @@ private:
 	vector<linePair*> lines;
 	vector<string> fastaFileNames;
 	vector<string> namefileNames;
+	vector<string> groupfileNames;
 	map<string, int> nameMap;
 	map<string, int>::iterator itNames;
 	
 	Classify* classify;
 	
-	string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir;
+	string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
 	int processors, kmerSize, numWanted, cutoff, iters;
 	float match, misMatch, gapOpen, gapExtend;
 	bool abort, probs;
@@ -57,6 +58,11 @@ private:
 	void appendTaxFiles(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<long>&);
+	#endif
 };
 
 #endif