X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=9a8706e82499fb80f9c2a55d61bc92c7b2399839;hb=d873f7bf94309317a08c8757e0d0d60b06fbd473;hp=2a673b0cb622bd97b8f91dc4f1c2e9c69de19e8d;hpb=692e0c1f69a78b568dc85cbdcea9fb6c189e2e6c;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 2a673b0..9a8706e 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -10,58 +10,125 @@
 #include "parsimony.h"
 
 /**************************************************************************************************/
+
 EstOutput Parsimony::getValues(Tree* t) {
 	try {
 		globaldata = GlobalData::getInstance();
+		vector<string> groups;
 		
-		data.resize(1,0);
-			
-		int score = 0;
-			
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-			int lc = t->tree[i].getLChild();
-			int rc = t->tree[i].getRChild();
-			
-			int iSize = 0;
-			int rcSize = 0;
-			int lcSize = 0;
-
-			//add in all the groups the users wanted
-			for (it = t->tree[i].pGroups.begin(); it != t->tree[i].pGroups.end(); it++) {
-				if (inUsersGroups(it->first) == true) {  iSize++;  }
+		copyTree = new Tree();
+		
+		//if the users enters no groups then give them the score of all groups
+		int numGroups = globaldata->Groups.size();
+		
+		//calculate number of comparsions
+		int numComp = 0;
+		for (int r=0; r<numGroups; r++) { 
+			for (int l = r+1; l < numGroups; l++) {
+				numComp++;
 			}
+		}
 
-			//if that leaves no groups give it 1 so it will cause no change to parent
-			if (iSize == 0) { iSize++; }
-			
-			//add in all the groups the users wanted
-			for (it = t->tree[rc].pGroups.begin(); it != t->tree[rc].pGroups.end(); it++) {
+		//numComp+1 for AB, AC, BC, ABC
+		data.resize(numComp+1,0);
+		
+		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);
 
-				if (inUsersGroups(it->first) == true) {  rcSize++;  }
-			}
+				//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();
 			
-			//if that leaves no groups give it 1 so it will cause no change to parent
-			if (rcSize == 0) { rcSize++; }
-
+					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++;
+					}
+				} 
 				
-			//add in all the groups the users wanted
-			for (it = t->tree[lc].pGroups.begin(); it != t->tree[lc].pGroups.end(); it++) {
-
-				if (inUsersGroups(it->first) == true) {  lcSize++;  }
+				data[count] = score;
+				count++;
+				groups.clear();
+			}
+		}
+		
+		if (numComp != 1) {
+			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]);
+					}
+				}
+			}else {
+				for (int i = 0; i < globaldata->Groups.size(); i++) {
+					groups.push_back(globaldata->Groups[i]);
+				}
 			}
 			
-			//if that leaves no groups give it 1 so it will cause no change to parent
-			if (lcSize == 0) { lcSize++; }
-
-
-			//if you have more groups than either of your kids then theres been a change.
-			 if(iSize > rcSize || iSize > lcSize){
-				score++;
-
+			//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++){
+//				cout << i << "..." << endl;
+				copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 			}
-		} 
 		
-		data[0] = score;
+//			map<string,int>::iterator it;
+			
+			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();
+				
+//				cout << i+1 << '\t' << lc+1 << '\t' << rc+1 << ":\t";
+				
+//				for(it=copyTree->tree[i].pGroups.begin();it!=copyTree->tree[i].pGroups.end();it++){
+//					cout << it->first << '\t';
+//				}
+				
+//				cout << " : " << iSize << '\t' << rcSize << '\t' << lcSize << '\t';
+					
+				//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++;
+				}
+//				cout << score << endl;
+			} 
+		
+			data[count] = score;
+			string hold;
+//			cin >> hold;
+		}
+		
+		delete copyTree;
 		
 		return data;
 	}
@@ -75,22 +142,6 @@ EstOutput Parsimony::getValues(Tree* t) {
 	}
 
 }
-/**************************************************************************************************/
 
-bool Parsimony::inUsersGroups(string groupname) {
-	try {
-		for (int i = 0; i < globaldata->Groups.size(); i++) {
-			if (groupname == globaldata->Groups[i]) { return true; }
-		}
-		return false;
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Parsimony class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
 /**************************************************************************************************/
+