fix weighted unifrac bug in findIndex and randomize labels

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 8fc5b3bcedd56c76200dfcb8889374906c9f28b3..a99459deeef74b6e99eab76c43b7a76787366b20 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -72,10 +72,10 @@ int UnifracWeightedCommand::execute() {
                        
                        //get scores for random trees
                        for (int j = 0; j < iters; j++) {
-                               int n = 1;
+//                             int n = 1;
                                int count = 0;
                                for (int r=0; r<numGroups; r++) { 
-                                       for (int l = n; l < numGroups; l++) {
+                                       for (int l = r+1; l < numGroups; l++) {
                                                //copy T[i]'s info.
                                                randT->getCopy(T[i]);
                                                 
@@ -90,18 +90,18 @@ int UnifracWeightedCommand::execute() {
                                                        //get wscore of random tree
                                                        randomData = weighted->getValues(randT, tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
                                                }
+//                                             randT->createNewickFile("hold"+toString(r)+toString(l)+toString(j));
 
                                                //save scores
                                                rScores[count].push_back(randomData[0]);
                                                validScores[count][randomData[0]] = randomData[0];
                                                count++;
                                        }
-                                       n++;
+//                                     n++;
                                }
                        }
 
                        removeValidScoresDuplicates(); 
-                       
                        //find the signifigance of the score for summary file
                        for (int f = 0; f < numComp; f++) {
                                //sort random scores
@@ -111,7 +111,7 @@ int UnifracWeightedCommand::execute() {
                                //so if you have 1000 random trees the index returned is 100 
                                //then there are 900 trees with a score greater then you. 
                                //giving you a signifigance of 0.900
-                               int index = findIndex(userData[f]);    if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code
+                               int index = findIndex(userData[f], f);    if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code
                        
                                //the signifigance is the number of trees with the users score or higher 
                                WScoreSig.push_back((iters-index)/(float)iters);
@@ -228,15 +228,12 @@ void UnifracWeightedCommand::removeValidScoresDuplicates() {
 }
 
 /***********************************************************/
-int UnifracWeightedCommand::findIndex(float score) {
+int UnifracWeightedCommand::findIndex(float score, int index) {
        try{
-               for (int e = 0; e < numComp; e++) {
-                       for (int i = 0; i < rScores[e].size(); i++) {
-//cout << rScores[e][i] << " number " << i << endl;
-                               if (rScores[e][i] >= score) { return i; }
-                       }
+               for (int i = 0; i < rScores[index].size(); i++) {
+                       if (rScores[index][i] >= score) {       return i;       }
                }
-               return -1;
+               return rScores[index].size();
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";