X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=b2809ed4b518b75618012dea74a0172ee2985589;hb=5318771152ee5b1a280b3dc50aedd887dd1da8a8;hp=3840514523002b545b7cf0f2fbb848b4c0ad0dd5;hpb=b2c44d69197045c26c1f4e62d248ab882c79a393;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 3840514..b2809ed 100644
--- 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;
 	}