changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 890085e53261ccf204a02b44fd6634e5020f0af0..1dc4c1bf0353609f3a18bc547ba947587d965fa7 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -43,12 +43,13 @@ private:
        vector<linePair*> lines;
        vector<string> fastaFileNames;
        vector<string> namefileNames;
-       map<string, int> nameMap;
-       map<string, int>::iterator itNames;
+       vector<string> groupfileNames;
+       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;
@@ -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