worked on unifrac.unweighted()

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index c345ca16bc478ee9635846c54abb8ab68ec67b69..f1326a82ca524a396f102bdeb8fa53f7264d971f 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -85,24 +85,21 @@ int UnifracUnweightedCommand::execute() {
                        
                        //get unweighted scores for random trees
                        for (int j = 0; j < iters; j++) {
-                               int count = 0;
-                               for (int r=0; r<numGroups; r++) { 
-                                       for (int l = r+1; l < numGroups; l++) {
-                                               //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
-                                               randomData = unweighted->getValues(randT, "", "");
-                       
-                                               //add trees unweighted score to map of scores
-                                               it2 = rscoreFreq[count].find(randomData[count]);
-                                               if (it2 != rscoreFreq[count].end()) {//already have that score
-                                                       rscoreFreq[count][randomData[count]]++;
-                                               }else{//first time we have seen this score
-                                                       rscoreFreq[count][randomData[count]] = 1;
-                                               }
+                               //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
+                               randomData = unweighted->getValues(randT, "", "");
                                
-                                               //add randoms score to validscores
-                                               validScores[count][randomData[count]] = randomData[count];
-                                               count++;
+                               for(int k = 0; k < numComp; k++) {      
+cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
+                                       //add trees unweighted score to map of scores
+                                       it2 = rscoreFreq[k].find(randomData[k]);
+                                       if (it2 != rscoreFreq[k].end()) {//already have that score
+                                               rscoreFreq[k][randomData[k]]++;
+                                       }else{//first time we have seen this score
+                                               rscoreFreq[k][randomData[k]] = 1;
                                        }
+                               
+                                       //add randoms score to validscores
+                                       validScores[k][randomData[k]] = randomData[k];
                                }
                        }
                
@@ -235,7 +232,7 @@ void UnifracUnweightedCommand::setGroups() {
                                        }
                                }else {
                                        for (int i = 0; i < globaldata->Groups.size(); i++) {
-                                               allGroups += tmap->namesOfGroups[i];
+                                               allGroups += globaldata->Groups[i];
                                                numGroups++;
                                        }
                                }