X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=d4b7e78ce01ba2b9e6507a2b5a502bae9dbb8b68;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=7f5122a66039c4dcd90c338dad078d11ce81e601;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 7f5122a..d4b7e78 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -1,6 +1,5 @@
 #ifndef ALIGNCOMMAND_H
 #define ALIGNCOMMAND_H
-
 /*
  *  aligncommand.h
  *  Mothur
@@ -10,7 +9,6 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 #include "database.hpp"
 #include "alignment.hpp"
@@ -25,7 +23,7 @@
 #include "nast.hpp"
 #include "nastreport.hpp"
 
-
+//test
 class AlignCommand : public Command {
 	
 public:
@@ -57,7 +55,6 @@ private:
 	
 	int driver(linePair*, string, string, string, string);
 	int createProcesses(string, string, string, string);
-	void appendAlignFiles(string, string); 
 	void appendReportFiles(string, string);
 	
 	#ifdef USE_MPI
@@ -120,7 +117,7 @@ struct alignData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){ 
 	alignData* pDataArray;
@@ -147,7 +144,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 		
 		pDataArray->count = pDataArray->end;
 		
-		AlignmentDB* templateDB = new AlignmentDB(templateFileName, 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;