X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=f806c8ded8b6c586e1592b004cd379eda2e79453;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=e5e9601781fdff5e35125b49de6ba452e180f9a2;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index e5e9601..f806c8d 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -177,7 +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();
 				
@@ -204,7 +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();
 						
@@ -213,7 +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;
@@ -221,6 +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;	
 						}
 					}
@@ -238,6 +240,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 				
 				report.print();
 				delete nast;
+                delete templateSeq;
 				if (needToDeleteCopy) {   delete copy;   }
 				
 				pDataArray->count++;
@@ -245,11 +248,11 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 			delete candidateSeq;
 			
 			//report progress
-			if((pDataArray->count) % 100 == 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
+			if((pDataArray->count) % 100 == 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n"); 	}
 			
 		}
 		//report progress
-		if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();		}
+		if((pDataArray->count) % 100 != 0){	pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");		}
 		
 		delete alignment;
 		delete templateDB;