X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.h;h=4e1b8d39f81dc067c60575d1938a21fd1de8dee0;hp=cfded3819156764fc86e49e9cb1977af9bb2ef48;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/aligncommand.h b/aligncommand.h
index cfded38..4e1b8d3 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -144,8 +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
@@ -161,7 +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; }
@@ -242,16 +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;