added mothurgetpid function. fixed bug with align.seqs related to g++ 4.8 change...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 4e1b8d39f81dc067c60575d1938a21fd1de8dee0..f806c8ded8b6c586e1592b004cd379eda2e79453 100644 (file)
--- 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++;