added distance option to summary.shared

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index 5f58f2eee439d16a11d2a2b9fbbb86397794b729..52d90c8ac4487d83acd1587b1d0f5c30b0c4cfe0 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -30,7 +30,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
                vector< vector<string> > namesOfGroupCombos;
                for (int i=0; i<numGroups; i++) { 
-                       for (int l = i+1; l < numGroups; l++) { 
+                       for (int l = 0; l < i; l++) {   
                                //initialize weighted scores
                                //WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
                                vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
@@ -51,12 +51,12 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
                                        if(i == processors - 1){
                                                numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
                                        }
-                                       lines.push_back(new linePair(startPos, numPairsPerProcessor));
+                                       lines.push_back(linePair(startPos, numPairsPerProcessor));
                                }
 
                                data = createProcesses(t, namesOfGroupCombos, sums);
                                
-                               for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+                               lines.clear();
                        }
                #else
                        data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums);
@@ -90,7 +90,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                        }else if (pid == 0){
        
                                EstOutput Myresults;
-                               Myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
+                               Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums);
                        
                                m->mothurOut("Merging results."); m->mothurOutEndLine();
                                
@@ -109,7 +109,7 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
                        }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
                }
        
-               results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums);
+               results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums);
        
                //force parent to wait until all the processes are done
                for (int i=0;i<(processors-1);i++) { 
@@ -196,6 +196,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                //calculate u for the group comb 
                int total = t->getNumNodes();
                int twentyPercent = (total * 0.20);
+               
                for(int i=0;i<t->getNumNodes();i++){
                        for (int h = start; h < (start+num); h++) {