update .gitignore

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index cfded3819156764fc86e49e9cb1977af9bb2ef48..f806c8ded8b6c586e1592b004cd379eda2e79453 100644 (file)
--- 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;