working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 4a5eb11bf320a500ddfca34f0504130637fda0f0..6236958a42a886bf5178aab8571f1513c596e00f 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -45,9 +45,9 @@ public:
        
 private:
        struct linePair {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
@@ -61,7 +61,7 @@ private:
        void appendReportFiles(string, string);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
        
        string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
@@ -86,15 +86,15 @@ typedef struct alignData {
        string align;
        string search;
        bool flip;
-       unsigned long int start;
-       unsigned long int end;
+       unsigned long long start;
+       unsigned long long end;
        MothurOut* m;
        //AlignmentDB* templateDB;
        float match, misMatch, gapOpen, gapExtend, threshold;
        int count, kmerSize, threadID;
        
        alignData(){}
-       alignData(string a, string r, string ac, string f, string al, string se, int ks, MothurOut* mout, unsigned long int st, unsigned long int en, bool fl, float ma, float misMa, float gapO, float gapE, float thr, int tid) {
+       alignData(string a, string r, string ac, string f, string al, string se, int ks, MothurOut* mout, unsigned long long st, unsigned long long en, bool fl, float ma, float misMa, float gapO, float gapE, float thr, int tid) {
                alignFName = a;
                reportFName = r;
                accnosFName = ac;