fixed parsimony with groups and worked on unifrac.unweighted with groups

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index b2809ed4b518b75618012dea74a0172ee2985589..0dea64e99a5f7bbe3adfe3dbd648ab8fb5365acf 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -14,17 +14,12 @@
 EstOutput Parsimony::getValues(Tree* t) {
        try {
                globaldata = GlobalData::getInstance();
+               vector<string> groups;
                
                copyTree = new Tree();
                
                //if the users enters no groups then give them the score of all groups
                int numGroups = globaldata->Groups.size();
-               if (numGroups == 0) { 
-                       numGroups++; 
-                       for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-                       }
-               }
                
                //calculate number of comparsions
                int numComp = 0;
@@ -36,7 +31,6 @@ EstOutput Parsimony::getValues(Tree* t) {
 
                //numComp+1 for AB, AC, BC, ABC
                data.resize(numComp+1,0);
-               vector<string> groups;
                
                int count = 0;
                for (int a=0; a<numGroups; a++) { 
@@ -77,35 +71,46 @@ EstOutput Parsimony::getValues(Tree* t) {
                        }
                }
                
-               //get score for all users groups
-               
-               //copy users tree so that you can redo pgroups 
-               copyTree->getCopy(t);
-               int score = 0;
+               if (numComp != 1) {
+                       if (numGroups == 0) {
+                               //get score for all users groups
+                               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+                                       groups.push_back(tmap->namesOfGroups[i]);
+                               }
+                       }else {
+                               for (int i = 0; i < globaldata->Groups.size(); i++) {
+                                       groups.push_back(globaldata->Groups[i]);
+                               }
+                       }
+                       
+                       //copy users tree so that you can redo pgroups 
+                       copyTree->getCopy(t);
+                       int score = 0;
                
-               //create pgroups that reflect the groups the user want to use
-               for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
-                       copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, globaldata->Groups));
-               }
+                       //create pgroups that reflect the groups the user want to use
+                       for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+                               copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
+                       }
                
-               for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
-                       int lc = copyTree->tree[i].getLChild();
-                       int rc = copyTree->tree[i].getRChild();
+                       for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+                               int lc = copyTree->tree[i].getLChild();
+                               int rc = copyTree->tree[i].getRChild();
                        
-                       int iSize = copyTree->tree[i].pGroups.size();
-                       int rcSize = copyTree->tree[rc].pGroups.size();
-                       int lcSize = copyTree->tree[lc].pGroups.size();
+                               int iSize = copyTree->tree[i].pGroups.size();
+                               int rcSize = copyTree->tree[rc].pGroups.size();
+                               int lcSize = copyTree->tree[lc].pGroups.size();
                
-                       //if isize are 0 then that branch is to be ignored
-                       if (iSize == 0) { }
-                       else if ((rcSize == 0) || (lcSize == 0)) { }
-                       //if you have more groups than either of your kids then theres been a change.
-                       else if(iSize > rcSize || iSize > lcSize){
-                               score++;
-                       }
-               } 
+                               //if isize are 0 then that branch is to be ignored
+                               if (iSize == 0) { }
+                               else if ((rcSize == 0) || (lcSize == 0)) { }
+                               //if you have more groups than either of your kids then theres been a change.
+                               else if(iSize > rcSize || iSize > lcSize){
+                                       score++;
+                               }
+                       } 
                
-               data[count] = score;
+                       data[count] = score;
+               }
                
                return data;
        }