X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=0487822764bbf36e11da5bd8faada1bba34a63c4;hb=b8f3e71c8a0310e25261464d27e6fcfe891483b0;hp=93efe2858aba11e852bd716f365bc653beea8b0d;hpb=0190105145fbd3e02da8f23cb50841229e5d696f;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 93efe28..0487822 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -10,54 +10,128 @@
 #include "parsimony.h"
 
 /**************************************************************************************************/
+
 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();
 		
-		data.resize(1,0);
+		//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);
+		
+		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++){
+				
+					if (m->control_pressed) { return data; }
+					
+					int lc = copyTree->tree[i].getLChild();
+					int rc = copyTree->tree[i].getRChild();
 			
-		int score = 0;
+					int iSize = copyTree->tree[i].pGroups.size();
+					int rcSize = copyTree->tree[rc].pGroups.size();
+					int lcSize = copyTree->tree[lc].pGroups.size();
 		
-		//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));
+					//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();
+			}
 		}
-		//hjkl
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
-			int lc = t->tree[i].getLChild();
-			int rc = t->tree[i].getRChild();
+		
+		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]);
+				}
+			}
 			
-			int iSize = t->tree[i].pGroups.size();
-			int rcSize = t->tree[rc].pGroups.size();
-			int lcSize = t->tree[lc].pGroups.size();
+			//copy users tree so that you can redo pgroups 
+			copyTree->getCopy(t);
+			int score = 0;
 		
-			//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++;
+			//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));
 			}
-			cout << i << ' ' << score << ": ";
-			t->tree[i].printNode();
-		} 
 		
-		string hold;
-		cin >> hold;
+//			map<string,int>::iterator it;
+			
+			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+			
+				if (m->control_pressed) { return data; }
+				
+				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;
+
+		}
 		
-		data[0] = score;
+		delete copyTree;
 		
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Parsimony", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 /**************************************************************************************************/