#include "nast.hpp"
#include "nastreport.hpp"
-
+//test
class AlignCommand : public Command {
public:
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct alignData {
+ string templateFileName;
string alignFName;
string reportFName;
string accnosFName;
int count, kmerSize, threadID;
alignData(){}
- 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) {
+ 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;
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
alignData* pDataArray;
pDataArray->count = pDataArray->end;
- AlignmentDB* templateDB = new AlignmentDB("saved-silent", pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
+ 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;