X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=f806c8ded8b6c586e1592b004cd379eda2e79453;hb=HEAD;hp=cfded3819156764fc86e49e9cb1977af9bb2ef48;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index cfded38..f806c8d 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; }
@@ -179,7 +177,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 				}
 				
 				Sequence temp = templateDB->findClosestSequence(candidateSeq);
-				Sequence* templateSeq = &temp;
+				Sequence* templateSeq = new Sequence(temp.getName(), temp.getAligned());
 				
 				float searchScore = templateDB->getSearchScore();
 				
@@ -206,7 +204,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 						
 						//rerun alignment
 						Sequence temp2 = templateDB->findClosestSequence(copy);
-						Sequence* templateSeq2 = &temp2;
+						Sequence* templateSeq2 = new Sequence(temp2.getName(), temp2.getAligned());
 						
 						searchScore = templateDB->getSearchScore();
 						
@@ -215,7 +213,8 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 						//check if any better
 						if (copy->getNumBases() > candidateSeq->getNumBases()) {
 							candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
-							templateSeq = templateSeq2; 
+							delete templateSeq;
+							templateSeq = templateSeq2;
 							delete nast;
 							nast = nast2;
 							needToDeleteCopy = true;
@@ -223,6 +222,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 						}else{  
 							wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 							delete nast2;
+                            delete templateSeq2;
 							delete copy;	
 						}
 					}
@@ -240,18 +240,19 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 				
 				report.print();
 				delete nast;
+                delete templateSeq;
 				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;