X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=b455761ed6fdcf2e8c11a6bcbb52b1704caee464;hb=941ee9f738e04d664ee8c5eb63e0dd3608cb5210;hp=6236958a42a886bf5178aab8571f1513c596e00f;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 6236958..b455761 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -25,7 +25,7 @@
 #include "nast.hpp"
 #include "nastreport.hpp"
 
-
+//test
 class AlignCommand : public Command {
 	
 public:
@@ -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;
@@ -94,7 +95,8 @@ typedef struct alignData {
 	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;
@@ -145,7 +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, 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;