changes to read.otu(list/shared) - took out substr calls

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index d19f862d340983786f00c25eaf02a6df30e0dea8..84f5f9f04d6752728c5f3bf72d5688cafd73b723 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -35,16 +35,18 @@ public:
        
 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;
+       map<string, vector<string> > nameMap;
+       map<string,  vector<string> >::iterator itNames;
        
        Classify* classify;
        
@@ -55,12 +57,12 @@ private:
        
        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<long>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 };