fixed bug in venn command

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 90ffb8df31d5aff2a47ee0f29ce9df33397d39b7..140aa6085b4007a3998ffc6a769b266464b16e6a 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -88,81 +88,87 @@ int DistanceCommand::execute(){
                
                remove(distFile.c_str());
                
-               if(processors == 1){
-                       driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);    
-               }       
-               else if(processors == 2){
+       //      #       if defined (WIN_VERSION)
+               //      driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
+       //      #       endif
                
-                       int pid = fork();
-                       if(pid > 0){
-                               driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);        
-                               appendFiles((distFile+"tempa"), distFile);
-                               remove((distFile + "tempa").c_str());   
-                       }
-                       else{
-                               driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);  
-                               appendFiles((distFile+"tempb"), distFile);
-                               remove((distFile + "tempb").c_str());   
-                       }
-                       wait(NULL);
-
-               }
-               else if(processors == 3){
-                       int pid1 = fork();
-                       if(pid1 > 0){
-                               int pid2 = fork();
-                               if(pid2 > 0){
-                                       driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
-                                       appendFiles(distFile+"tempa", distFile);
+       //      #       if defined (LINUX_VERSION)
+                       if(processors == 1){
+                               driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);    
+                       }       
+                       else if(processors == 2){
+               
+                               int pid = fork();
+                               if(pid > 0){
+                                       driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);        
+                                       appendFiles((distFile+"tempa"), distFile);
                                        remove((distFile + "tempa").c_str());   
                                }
                                else{
-                                       driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);        
-                                       appendFiles(distFile+"tempb", distFile);
-                                       remove((distFile + "tempb").c_str());                           
+                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);  
+                                       appendFiles((distFile+"tempb"), distFile);
+                                       remove((distFile + "tempb").c_str());   
                                }
                                wait(NULL);
+
                        }
-                       else{
-                               driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);      
-                               appendFiles(distFile+"tempc", distFile);
-                               remove((distFile + "tempc").c_str());                   
-                       }
-                       wait(NULL);
-               }
-               else if(processors == 4){
-                       int pid1 = fork();
-                       if(pid1 > 0){
-                               int pid2 = fork();
-                               if(pid2 > 0){
-                                       driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);      
-                                       appendFiles(distFile+"tempa", distFile);
-                                       remove((distFile + "tempa").c_str());                   
+                       else if(processors == 3){
+                               int pid1 = fork();
+                               if(pid1 > 0){
+                                       int pid2 = fork();
+                                       if(pid2 > 0){
+                                               driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
+                                               appendFiles(distFile+"tempa", distFile);
+                                               remove((distFile + "tempa").c_str());   
+                                       }
+                                       else{
+                                               driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);        
+                                               appendFiles(distFile+"tempb", distFile);
+                                               remove((distFile + "tempb").c_str());                           
+                                       }
+                                       wait(NULL);
                                }
                                else{
-                                       driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);      
-                                       appendFiles(distFile+"tempb", distFile);
-                                       remove((distFile + "tempb").c_str());                           
+                                       driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);      
+                                       appendFiles(distFile+"tempc", distFile);
+                                       remove((distFile + "tempc").c_str());                   
                                }
                                wait(NULL);
                        }
-                       else{
-                               int pid3 = fork();
-                               if(pid3 > 0){
-                                       driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);  
-                                       appendFiles(distFile+"tempc", distFile);
-                                       remove((distFile + "tempc").c_str());                           
+                       else if(processors == 4){
+                               int pid1 = fork();
+                               if(pid1 > 0){
+                                       int pid2 = fork();
+                                       if(pid2 > 0){
+                                               driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);      
+                                               appendFiles(distFile+"tempa", distFile);
+                                               remove((distFile + "tempa").c_str());                   
+                                       }
+                                       else{
+                                               driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);      
+                                               appendFiles(distFile+"tempb", distFile);
+                                               remove((distFile + "tempb").c_str());                           
+                                       }
+                                       wait(NULL);
                                }
                                else{
-                                       driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);    
-                                       appendFiles(distFile+"tempd", distFile);
-                                       remove((distFile + "tempd").c_str());                           
+                                       int pid3 = fork();
+                                       if(pid3 > 0){
+                                               driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);  
+                                               appendFiles(distFile+"tempc", distFile);
+                                               remove((distFile + "tempc").c_str());                           
+                                       }
+                                       else{
+                                               driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);    
+                                               appendFiles(distFile+"tempd", distFile);
+                                               remove((distFile + "tempd").c_str());                           
+                                       }
+                                       wait(NULL);
                                }
                                wait(NULL);
                        }
                        wait(NULL);
-               }
-               wait(NULL);
+               //#     endif
        
                delete distCalculator;
        
@@ -191,7 +197,11 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
        
                for(int i=startLine;i<endLine;i++){
                
-                       for(int j=0;j<i;j++){   
+                       for(int j=0;j<i;j++){
+//cout << "unaligned" << endl;
+//cout << align->get(i).getUnaligned() << "  " << align->get(j).getUnaligned() << endl;
+//cout << "aligned" << endl;
+//cout << align->get(i).getAligned() << "  " << align->get(j).getAligned() << endl;
                                distCalculator->calcDist(align->get(i), align->get(j));
                                double dist = distCalculator->getDist();