parsimony with groups

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 3840514523002b545b7cf0f2fbb848b4c0ad0dd5..b2809ed4b518b75618012dea74a0172ee2985589 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -15,22 +15,86 @@ EstOutput Parsimony::getValues(Tree* t) {
        try {
                globaldata = GlobalData::getInstance();
                
-               data.resize(1,0);
+               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;
+               for (int r=0; r<numGroups; r++) { 
+                       for (int l = r+1; l < numGroups; l++) {
+                               numComp++;
+                       }
+               }
+
+               //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++) { 
+                       for (int l = a+1; l < numGroups; l++) {
+                               int score = 0;
+                               
+                               //groups in this combo
+                               groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+                               
+                               //copy users tree so that you can redo pgroups 
+                               copyTree->getCopy(t);
+
+                               //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();
                        
+                                       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++;
+                                       }
+                               } 
+                               
+                               data[count] = score;
+                               count++;
+                               groups.clear();
+                       }
+               }
+               
+               //get score for all users groups
+               
+               //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=t->getNumLeaves();i<t->getNumNodes();i++){
-                       t->tree[i].pGroups = (t->mergeUserGroups(i));
+               for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+                       copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, globaldata->Groups));
                }
                
-               for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-                       int lc = t->tree[i].getLChild();
-                       int rc = t->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 = t->tree[i].pGroups.size();
-                       int rcSize = t->tree[rc].pGroups.size();
-                       int lcSize = t->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) { }
@@ -41,8 +105,7 @@ EstOutput Parsimony::getValues(Tree* t) {
                        }
                } 
                
-               
-               data[0] = score;
+               data[count] = score;
                
                return data;
        }