X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=5432d00564b2151fabaf09e9d16258dff0d298ae;hb=b866e1519a60681527244036428104ad1cb90c93;hp=fa1bf57468e31c114224841019b338020e574b21;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index fa1bf57..5432d00 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:
@@ -36,6 +34,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "align.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
 	string getDescription()		{ return "align sequences"; }
@@ -57,7 +56,6 @@ 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
@@ -79,6 +77,7 @@ private:
 // 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;
@@ -94,7 +93,8 @@ 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;
@@ -118,7 +118,7 @@ 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;
@@ -145,7 +145,7 @@ 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;