X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=86bb4d7a4377904f0ca3c2712204d5932fdb46f6;hb=110ed3a070bf6b602cccef89c8626cce033315d3;hp=193eeacae57c5bb62deb844bac610b40437d14a2;hpb=d3aed959ca3b68890eeb7b815e24210bcfeb256c;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 193eeac..86bb4d7 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -1,6 +1,6 @@
 #ifndef ALIGNCOMMAND_H
 #define ALIGNCOMMAND_H
-
+//test
 /*
  *  aligncommand.h
  *  Mothur
@@ -10,7 +10,6 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 #include "database.hpp"
 #include "alignment.hpp"
@@ -25,7 +24,7 @@
 #include "nast.hpp"
 #include "nastreport.hpp"
 
-
+//test
 class AlignCommand : public Command {
 	
 public:
@@ -45,9 +44,9 @@ 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 +60,7 @@ 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 +77,8 @@ 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 +86,16 @@ 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;
@@ -113,11 +114,12 @@ typedef struct alignData {
 		search = se;
 		count = 0;
 		kmerSize = ks;
+		threadID = tid;
 	}
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){ 
 	alignData* pDataArray;
@@ -144,7 +146,7 @@ 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;