finished dereplicate changes to chimera commands. added taxonomy file to subsample...

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 767fdb52702bd1a3652d6bf2c1e2b244958e48ca..e937b1661b90b5f8e3340178222c21a9a9cd8d9e 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -643,7 +643,8 @@ 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();
@@ -672,11 +673,18 @@ 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 (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'; }
@@ -690,7 +698,7 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                        
                }
                m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               
+               cout << "num less than 0.01 = " << countSmall << " of " << countAll << endl;
                outFile.close();
         delete alignment;
         delete distCalculator;