working on unifrac parallelization

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index ad012b542b82a99ad0ac40782688c325360268b0..5a2a5ec5c504796869b7f0392e6709e66eb62e9f 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -192,22 +192,24 @@ int UnifracWeightedCommand::execute() {
                                
                                //get scores for random trees
                                for (int j = 0; j < iters; j++) {
-                                       int count = 0;
                                        
                                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                                if(processors == 1){
                                                        driver(T[i], randT, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
                                                }else{
                                                        createProcesses(T[i], randT, namesOfGroupCombos, sums, rScores);
-                                                       for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                                }
                                        #else
                                                driver(T[i], randT, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
                                        #endif
                                        
                                        if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());  } return 0; }
+                                       
+                                       //report progress
+                                       m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();          
                                }
-                               
+
+                               for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                
                                //find the signifigance of the score for summary file
                                for (int f = 0; f < numComp; f++) {
@@ -290,14 +292,12 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector
                                process++;
                        }else if (pid == 0){
                                driver(t, randT, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums, scores);
-                               
-                               m->mothurOut("Merging results."); m->mothurOutEndLine();
-                               
+                       
                                //pass numSeqs to parent
                                ofstream out;
                                string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
                                m->openOutputFile(tempFile, out);
-                               for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) {  out << scores[i][0] << '\t';  } out << endl;
+                               for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) {  out << scores[i][(scores[i].size()-1)] << '\t';  } out << endl;
                                out.close();
                                
                                exit(0);
@@ -318,13 +318,12 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector
                        string s = outputDir + toString(processIDS[i]) + ".weightedcommand.results.temp";
                        m->openInputFile(s, in);
                        
-                       for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { in >> scores[i][0]; }
+                       double tempScore;
+                       for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { in >> tempScore; scores[i].push_back(tempScore); }
                        in.close();
                        remove(s.c_str());
                }
                
-               m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
-               
                return 0;
 #endif         
        }
@@ -337,12 +336,9 @@ int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector
 /**************************************************************************************************/
 int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) { 
  try {
-               int count = 0;
-               int total = num;
-               int twentyPercent = (total * 0.20);
-
+       
                for (int h = start; h < (start+num); h++) {
-               
+       cout << "doing " << h << endl;  
                        if (m->control_pressed) { return 0; }
                
                        //initialize weighted score
@@ -365,15 +361,8 @@ int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string>
                                                                                
                        //save scores
                        scores[h].push_back(randomData[0]);
-                       
-                       count++;
-
-                       //report progress
-                       if((count) % twentyPercent == 0){       m->mothurOut("Random comparison percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine();         }
                }
                
-               m->mothurOut("Random comparison percentage complete: 100"); m->mothurOutEndLine();
-               
                return 0;
 
        }