changed groupfile in classify.seqs to reflect multiple fasta files

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 19fc8a011d9b3dbc8dd8f1e482f7b50dc100078f..639ae6543082a7162b270da16137078da5c8e362 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -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