added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 6ec6c57823a9055b6b70a97b9b9b06b6bb00074b..49a73505c3df0c77b4ff3fe0b6e71f038eb5f13c 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -17,15 +17,16 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
                outputDir = o;
                
                //if the users enters no groups then give them the score of all groups
-               int numGroups = m->Groups.size();
+               vector<string> mGroups = m->getGroups();
+               int numGroups = mGroups.size();
                
                //calculate number of comparsions
                int numComp = 0;
                vector< vector<string> > namesOfGroupCombos;
                for (int r=0; r<numGroups; r++) { 
-                       for (int l = r+1; l < numGroups; l++) {
+                       for (int l = 0; l < r; l++) {
                                numComp++;
-                               vector<string> groups; groups.push_back(m->Groups[r]); groups.push_back(m->Groups[l]);
+                               vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
                                //cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
                                namesOfGroupCombos.push_back(groups);
                        }
@@ -36,16 +37,17 @@ EstOutput Parsimony::getValues(Tree* t, int p, string o) {
                        vector<string> groups;
                        if (numGroups == 0) {
                                //get score for all users groups
-                               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                                       if (tmap->namesOfGroups[i] != "xxx") {
-                                               groups.push_back(tmap->namesOfGroups[i]);
+                               vector<string> tGroups = tmap->getNamesOfGroups();
+                               for (int i = 0; i < tGroups.size(); i++) {
+                                       if (tGroups[i] != "xxx") {
+                                               groups.push_back(tGroups[i]);
                                                //cout << tmap->namesOfGroups[i] << endl;
                                        }
                                }
                                namesOfGroupCombos.push_back(groups);
                        }else {
-                               for (int i = 0; i < m->Groups.size(); i++) {
-                                       groups.push_back(m->Groups[i]);
+                               for (int i = 0; i < mGroups.size(); i++) {
+                                       groups.push_back(mGroups[i]);
                                        //cout << globaldata->Groups[i] << endl;
                                }
                                namesOfGroupCombos.push_back(groups);