X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=f874e9a869d269546c04ce8fd9648786dcc4bab1;hp=e937b1661b90b5f8e3340178222c21a9a9cd8d9e;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=037b7fccc64a5c7d5d5c23a949273a912160a400

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index e937b16..f874e9a 100644
--- 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);
 			
@@ -643,8 +643,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
 		outFile << setprecision(4);
 		
 		if((output == "lt") && startLine == 0){	outFile << alignDB.getNumSeqs() << endl;	}
-		int countSmall = 0;
-        int countAll = 0;
+		
 		for(int i=startLine;i<endLine;i++){
 			if(output == "lt")	{	
 				string name = alignDB.get(i).getName();
@@ -672,19 +671,13 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
 				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 				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 (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
 				                
 				if(dist <= cutoff){
-                    if (dist < 0.01) { countSmall++; }
-                    countAll++;
-
 					if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 				}
 				if (output == "lt") {  outFile << dist << '\t'; }
@@ -693,12 +686,12 @@ 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();
-		cout << "num less than 0.01 = " << countSmall << " of " << countAll << endl;
+		m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+		
 		outFile.close();
         delete alignment;
         delete distCalculator;
@@ -781,17 +774,19 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
 								
-				outFile << dist << '\t'; 
+				outFile << dist << '\t';
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
 			}
 			
 			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;
@@ -864,6 +859,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
 				
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
+                
+                if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
 				
 				if(dist <= cutoff){
 					 outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); 
@@ -972,6 +969,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 				
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
+                
+                if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
 				
 				outputString += toString(dist) + "\t"; 
 			}
@@ -1076,7 +1075,9 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 				distCalculator->calcDist(seqI, seqJ);
 				double dist = distCalculator->getDist();
 				
-				outputString += toString(dist) + "\t"; 
+				outputString += toString(dist) + "\t";
+                
+                if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' +  alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
 			}
 			
 			outputString += "\n";