another attempt to fix sffinfo

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 0ddfc1c6229758991e74b0def36a778182a74da6..93707458d3b7b7b09cd1b4eb3aa02f8f03bafa16 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -29,9 +29,9 @@ public:
 private:
 
        struct linePair {
-               int start;
+               unsigned long int start;
                int numSeqs;
-               linePair(long 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;
@@ -40,13 +40,15 @@ private:
        int createProcesses(string, string, 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
 
-       bool abort, filter, MPIWroteAccnos;
-       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir;
+       bool abort, filter;
+       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;
+       vector<string> outputNames;
+       vector<string> fastaFileNames;
        
        
 };