X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pairwiseseqscommand.h;h=90c21b25a7c35c47834ea7311f3e7f969163fc98;hp=defccb5227104798667b49c879617bf9d1811200;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=b740fb182372143e152143c6cc5b9ac8591f09b7

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index defccb5..90c21b2 100644
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -193,17 +193,19 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
                 
+                if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
+                
 				outFile << dist << '\t'; 
 			}
 			
 			outFile << endl; 
 			
 			if(i % 100 == 0){
-				pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+				pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 			}
 			
 		}
-		pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+		pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
 		
 		outFile.close();
         delete alignment;
@@ -293,6 +295,8 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
                 
+                if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
+                
 				if(dist <= pDataArray->cutoff){
 					if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
 				}
@@ -302,11 +306,11 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 			if (pDataArray->output == "lt") { outFile << endl; }
 			
 			if(i % 100 == 0){
-				pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+				pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 			}
 			
 		}
-		pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+		pDataArray->m->mothurOutJustToScreen(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)+"\n");
 		
 		outFile.close();
         delete alignment;