changes while testing

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index defccb5227104798667b49c879617bf9d1811200..90c21b25a7c35c47834ea7311f3e7f969163fc98 100644 (file)
--- 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;