X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=f806c8ded8b6c586e1592b004cd379eda2e79453;hb=HEAD;hp=d4b7e78ce01ba2b9e6507a2b5a502bae9dbb8b68;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index d4b7e78..f806c8d 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -34,7 +34,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "align.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
 	string getDescription()		{ return "align sequences"; }
 	
@@ -142,8 +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
@@ -159,7 +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; }
@@ -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;	
 						}
 					}
@@ -238,18 +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;