X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.h;h=4e1b8d39f81dc067c60575d1938a21fd1de8dee0;hp=b455761ed6fdcf2e8c11a6bcbb52b1704caee464;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=941ee9f738e04d664ee8c5eb63e0dd3608cb5210

diff --git a/aligncommand.h b/aligncommand.h
index b455761..4e1b8d3 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"
@@ -36,7 +34,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "align.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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 +57,6 @@ 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 +119,7 @@ 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;
@@ -145,8 +144,6 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 			inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
 		}
 		
-		pDataArray->count = pDataArray->end;
-		
 		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
@@ -162,7 +159,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 			alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase);
 		}
 		
-		int count = 0;
+		pDataArray->count = 0;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 			
 			if (pDataArray->m->control_pressed) {  break; }
@@ -243,16 +240,16 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 				delete nast;
 				if (needToDeleteCopy) {   delete copy;   }
 				
-				count++;
+				pDataArray->count++;
 			}
 			delete candidateSeq;
 			
 			//report progress
-			if((count) % 100 == 0){	pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine();		}
+			if((pDataArray->count) % 100 == 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); 	}
 			
 		}
 		//report progress
-		if((count) % 100 != 0){	pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine();		}
+		if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");		}
 		
 		delete alignment;
 		delete templateDB;