added countgaps parameter to chop.seqs command

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index d19f862d340983786f00c25eaf02a6df30e0dea8..03e6826d1276b4efbdf12b5fce0aeb4cdea8fb08 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -35,16 +35,17 @@ public:
        
 private:
        struct linePair {
-               int start;
+               unsigned long int start;
                int numSeqs;
-               linePair(int i, int j) : start(i), numSeqs(j) {}
+               linePair(unsigned long int i, int j) : start(i), numSeqs(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;
+       map<string, vector<string> > nameMap;
+       map<string,  vector<string> >::iterator itNames;
        
        Classify* classify;
        
@@ -60,7 +61,7 @@ private:
        
        int MPIReadNamesFile(string);
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 };