changes while testing

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 767fdb52702bd1a3652d6bf2c1e2b244958e48ca..7d96e31d1eefb534729e421b266092db1536aa46 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -564,7 +564,7 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
                        string extension = toString(i) + ".temp";
 
                        // Allocate memory for thread data.
-                       pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
+                       pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, i);
                        pDataArray.push_back(tempDist);
                        processIDS.push_back(i);
                        
@@ -672,10 +672,14 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                                seqI.setAligned(alignment->getSeqAAln());
                                seqJ.setAligned(alignment->getSeqBAln());
 
-                               
+                               //cout << seqI.getName() << '\t' << seqJ.getName() << endl;
+                //cout << alignment->getSeqAAln() << endl << alignment->getSeqBAln() << endl;
+                
                                distCalculator->calcDist(seqI, seqJ);
                                double dist = distCalculator->getDist();
-                               
+                
+                //cout << "dist = " << dist << endl;
+                                               
                                if(dist <= cutoff){
                                        if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
                                }
@@ -685,11 +689,11 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                        if (output == "lt") { outFile << endl; }
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
         delete alignment;
@@ -779,11 +783,11 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
                        outFile << endl; 
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
         delete alignment;