X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.h;h=115360f7d5c3015130b0beef8a704f7669a382b5;hb=0d4b21e5ccc56276b0c18d17d8e75d94ce1df4e7;hp=19fc8a011d9b3dbc8dd8f1e482f7b50dc100078f;hpb=c3f0a9c8f932b923f3a6fbbf143e8f4b85fd6f5f;p=mothur.git

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 19fc8a0..115360f 100644
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,7 +12,6 @@
 
 #include "mothur.h"
 #include "command.hpp"
-//#include "alignment.hpp"
 #include "classify.h"
 
 //KNN and Bayesian methods modeled from algorithms in
@@ -28,35 +27,52 @@
 class ClassifySeqsCommand : public Command {
 	
 public:
-	ClassifySeqsCommand(string);	
+	ClassifySeqsCommand(string);
+	ClassifySeqsCommand();
 	~ClassifySeqsCommand();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "classify.seqs";		}
+	string getCommandCategory()		{ return "Phylotype Analysis";	}
+	string getHelpString();	
+	
 	int execute(); 
-	void help();	
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	
 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;
-	map<string, int> nameMap;
-	map<string, int>::iterator itNames;
+	vector<string> groupfileNames;
+	vector<string> outputNames;
+	map<string, vector<string> > nameMap;
+	map<string,  vector<string> >::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;
 	
 	int driver(linePair*, string, string, string);
 	void appendTaxFiles(string, string);
-	void createProcesses(string, 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