unifrac parallelization done, changed dist.seqs output=square to calc all distance...

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 7836eb682f19d444ae2ffb7f82fe538efdb7d933..a50d147de23d7cbc882be909e4a78870a867d4c3 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -160,7 +160,7 @@ int UnifracUnweightedCommand::execute() {
                        UWScoreSig.resize(numComp); 
 
                        userData = unweighted->getValues(T[i], processors, outputDir);  //userData[0] = unweightedscore
-                       
+               
                        if (m->control_pressed) { if (random) { delete output;  } outSum.close();  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  }return 0; }
                        
                        //output scores for each combination
@@ -171,18 +171,14 @@ int UnifracUnweightedCommand::execute() {
                                //add users score to validscores
                                validScores[userData[k]] = userData[k];
                        }
-                       
+               
                        //get unweighted scores for random trees - if random is false iters = 0
                        for (int j = 0; j < iters; j++) {
+               
                                //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
-                               randomData = unweighted->getValues(T[i], "", "");
+                               randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
                                
-                               if (m->control_pressed) { 
-                                       if (random) { delete output;  }
-                                       outSum.close();
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
-                                       return 0; 
-                               }
+                               if (m->control_pressed) { if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
                        
                                for(int k = 0; k < numComp; k++) {      
                                        //add trees unweighted score to map of scores
@@ -196,6 +192,9 @@ int UnifracUnweightedCommand::execute() {
                                        //add randoms score to validscores
                                        validScores[randomData[k]] = randomData[k];
                                }
+                               
+                               //report progress
+                               m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();  
                        }
        
                        for(int a = 0; a < numComp; a++) {
@@ -216,13 +215,7 @@ int UnifracUnweightedCommand::execute() {
        
                        }
                        
-                       
-                       if (m->control_pressed) { 
-                               if (random) { delete output;  }
-                               outSum.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
-                               return 0; 
-                       }
+                       if (m->control_pressed) { if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0;  }
                        
                        //print output files
                        printUWSummaryFile(i);
@@ -299,16 +292,16 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) {
                                if (UWScoreSig[a][0] > (1/(float)iters)) {
                                        outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
                                        cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; 
-                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t" + toString(UWScoreSig[a][0])); m->mothurOutEndLine(); 
+                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t" + toString(UWScoreSig[a][0])+ "\n"); 
                                }else {
                                        outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
                                        cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; 
-                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters)))); m->mothurOutEndLine();
+                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters))) + "\n"); 
                                }
                        }else{
                                outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
                                cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl; 
-                               m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00"); m->mothurOutEndLine();
+                               m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00\n");
                        }
                }