added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 193eeacae57c5bb62deb844bac610b40437d14a2..d42369520f127a8ba06c1c86ae9e9929c20f4fac 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;
@@ -78,7 +78,8 @@ private:
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct alignData {
+struct alignData {
+       string templateFileName;
        string alignFName; 
        string reportFName; 
        string accnosFName;
@@ -86,15 +87,16 @@ 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;
+       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) {
+       alignData(string te, 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) {
+               templateFileName = te;
                alignFName = a;
                reportFName = r;
                accnosFName = ac;
@@ -113,6 +115,7 @@ typedef struct alignData {
                search = se;
                count = 0;
                kmerSize = ks;
+               threadID = tid;
        }
 };
 
@@ -144,7 +147,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
                
                pDataArray->count = pDataArray->end;
                
-               AlignmentDB* templateDB = new AlignmentDB("saved-silent", pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch);
+               AlignmentDB* templateDB = new AlignmentDB(pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
                
                //moved this into driver to avoid deep copies in windows paralellized version
                Alignment* alignment;