changed groupfile in classify.seqs to reflect multiple fasta files

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index a73aa0c576f1dc6a3437d9c37557aa89cc0b451c..639ae6543082a7162b270da16137078da5c8e362 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,13 +12,23 @@
 
 #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();    
@@ -31,17 +41,28 @@ private:
        };
        vector<int> processIDS;   //processid
        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, 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); 
+       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