X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=405dfd2b3feaf4c1a5327526936a7baaaa4aba0a;hb=8fd4a602269974e6548f4a387dddd6bd80a999ab;hp=a7cf9c9092e6b8565f538d38b2f86ae4a75b5944;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index a7cf9c9..405dfd2 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -13,63 +13,363 @@
 
 EstOutput Unweighted::getValues(Tree* t) {
 	try {
+		globaldata = GlobalData::getInstance();
+		
+		vector<string> groups;
+		double UniqueBL;  //a branch length is unique if it's chidren are from the same group
+		double totalBL;	//all branch lengths
+		double UW;		//Unweighted Value = UniqueBL / totalBL;
+		map<string, int>::iterator it;  //iterator to traverse pgroups
+		map<string, int> copyIpcount;
+
 	
-		//clear out old values
-		data.resize(1,0); 
-		penalty.resize(t->getNumLeaves(), 0);
-		
-		map<string,double> unique;  //group, total of all branch lengths of nodes with that group.
-		double shared = 0.0000;
-		double UW=0.0000;
-		
-		//add up the branch lengths for each group. 
-		for(int i=0;i<t->getNumLeaves();i++){
-			if(t->tree[i].pGroups.size() > 0){
-				unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+		//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++;
 			}
 		}
+
+		//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++) {
+				UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
+				totalBL = 0.00;	//all branch lengths
+				UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
+				copyIpcount.clear();
+				
+				//groups in this combo
+				groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 		
-		//for each non-leaf node
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+				for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
 		
-			int lc = t->tree[i].getLChild();  //lc = vector index of left child
-			int rc = t->tree[i].getRChild();  //rc = vector index of right child
+					int lc = t->tree[i].getLChild();  //lc = vector index of left child
+					int rc = t->tree[i].getRChild();  //rc = vector index of right child
+			
+					/**********************************************************************/
+					//This section adds in all lengths that are non leaf
+			
+					copyIpcount = t->tree[i].pcount;
+					for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
+						if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+					}
+			
+					//if i's children are from the same group then i's pcount size will be 1 
+					//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+					if (copyIpcount.size() == 0) { }
+					else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += t->tree[i].getBranchLength();	}
+			
+					//add i's BL to total if it is from the groups the user wants
+					if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
+						totalBL += t->tree[i].getBranchLength(); 
+					}
+			
+					/**********************************************************************/
+					//This section adds in all lengths that are leaf
+			
+					//if i's chidren are leaves
+					if (t->tree[rc].getRChild() == -1) {
+						//if rc is a valid group and rc has a BL
+						if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+							UniqueBL += t->tree[rc].getBranchLength();
+							totalBL += t->tree[rc].getBranchLength(); 
+						}
+					}
+			
+					if (t->tree[lc].getLChild() == -1) {
+						//if lc is a valid group and lc has a BL
+						if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+							UniqueBL += t->tree[lc].getBranchLength();
+							totalBL += t->tree[lc].getBranchLength(); 
+						}
+					}
 			
-			//get penalty values
-			if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
-				penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+					/**********************************************************************/
+				}
+		
+				UW = (UniqueBL / totalBL);  
+	
+				if (isnan(UW) || isinf(UW)) { UW = 0; }
+	
+				data[count] = UW;
+				count++;
+				groups.clear();
 			}
-			else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
-				penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
+		}
+		
+		
+		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]);
+				}
 			}
-			else{
-				penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+		
+			UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
+			totalBL = 0.00;	//all branch lengths
+			UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
+			copyIpcount.clear();
+				
+			for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+		
+				int lc = t->tree[i].getLChild();  //lc = vector index of left child
+				int rc = t->tree[i].getRChild();  //rc = vector index of right child
+			
+				/**********************************************************************/
+				//This section adds in all lengths that are non leaf
+			
+				copyIpcount = t->tree[i].pcount;
+				for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
+					if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+				}
+			
+				//if i's children are from the same group then i's pcount size will be 1 
+				//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+				if (copyIpcount.size() == 0) { }
+				else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += t->tree[i].getBranchLength();	}
+			
+				//add i's BL to total if it is from the groups the user wants
+				if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
+					totalBL += t->tree[i].getBranchLength(); 
+				}
+			
+				/**********************************************************************/
+				//This section adds in all lengths that are leaf
+			
+				//if i's chidren are leaves
+				if (t->tree[rc].getRChild() == -1) {
+					//if rc is a valid group and rc has a BL
+					if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+						UniqueBL += t->tree[rc].getBranchLength();
+						totalBL += t->tree[rc].getBranchLength(); 
+					}
+				}
+			
+				if (t->tree[lc].getLChild() == -1) {
+					//if lc is a valid group and lc has a BL
+					if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+						UniqueBL += t->tree[lc].getBranchLength();
+						totalBL += t->tree[lc].getBranchLength(); 
+					}
+				}
+			
+				/**********************************************************************/
 			}
+		
+			UW = (UniqueBL / totalBL);  
+	
+			if (isnan(UW) || isinf(UW)) { UW = 0; }
+	
+			data[count] = UW;
+		}
 
-			//not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
-			if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
-				shared -= 1; 
-			}
-			else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
-				shared += t->tree[i].getBranchLength();
-			}
-			else if( t->tree[i].pGroups.size() != 0){
-				unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();	    
+		return data;
+	
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}
+
+/**************************************************************************************************/
+
+EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) { 
+ try {
+	globaldata = GlobalData::getInstance();
+		
+		vector<string> groups;
+		double UniqueBL;  //a branch length is unique if it's chidren are from the same group
+		double totalBL;	//all branch lengths
+		double UW;		//Unweighted Value = UniqueBL / totalBL;
+		map<string, int>::iterator it;  //iterator to traverse pgroups
+		map<string, int> copyIpcount;
+		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++;
 			}
 		}
-    
-		map<string,double>::iterator pos;
-		for(pos=unique.begin();pos!=unique.end();pos++){
-			if(pos->first!="xxx"){	    
-				UW += unique[pos->first];
+
+		//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++) {
+				UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
+				totalBL = 0.00;	//all branch lengths
+				UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
+				copyIpcount.clear();
+				
+				//copy random tree passed in
+				copyTree->getCopy(t);
+								
+				//groups in this combo
+				groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+				
+				//swap labels in the groups you want to compare
+				copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
+				
+				//copyTree->createNewickFile("random"+groupA+toString(count));
+		
+				for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+		
+					int lc = copyTree->tree[i].getLChild();  //lc = vector index of left child
+					int rc = copyTree->tree[i].getRChild();  //rc = vector index of right child
+			
+					/**********************************************************************/
+					//This section adds in all lengths that are non leaf
+			
+					copyIpcount = copyTree->tree[i].pcount;
+					for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
+						if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+					}
+			
+					//if i's children are from the same group then i's pcount size will be 1 
+					//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+					if (copyIpcount.size() == 0) { }
+					else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += copyTree->tree[i].getBranchLength();	}
+			
+					//add i's BL to total if it is from the groups the user wants
+					if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
+						totalBL += copyTree->tree[i].getBranchLength(); 
+					}
+			
+					/**********************************************************************/
+					//This section adds in all lengths that are leaf
+			
+					//if i's chidren are leaves
+					if (copyTree->tree[rc].getRChild() == -1) {
+						//if rc is a valid group and rc has a BL
+						if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+							UniqueBL += copyTree->tree[rc].getBranchLength();
+							totalBL += copyTree->tree[rc].getBranchLength(); 
+						}
+					}
+			
+					if (copyTree->tree[lc].getLChild() == -1) {
+						//if lc is a valid group and lc has a BL
+						if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+							UniqueBL += copyTree->tree[lc].getBranchLength();
+							totalBL += copyTree->tree[lc].getBranchLength(); 
+						}
+					}
+			
+					/**********************************************************************/
+				}
+		
+				UW = (UniqueBL / totalBL);  
+	
+				if (isnan(UW) || isinf(UW)) { UW = 0; }
+	
+				data[count] = UW;
+				count++;
+				groups.clear();
 			}
 		}
+		
+		
+		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]);
+				}
+			}
+		
+			UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
+			totalBL = 0.00;	//all branch lengths
+			UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
+			copyIpcount.clear();
+		
+			//copy random tree passed in
+			copyTree->getCopy(t);
+				
+			//swap labels in all the groups you want to compare
+			copyTree->assembleRandomUnifracTree(groups);
+
+			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+		
+				int lc = copyTree->tree[i].getLChild();  //lc = vector index of left child
+				int rc = copyTree->tree[i].getRChild();  //rc = vector index of right child
+			
+				/**********************************************************************/
+				//This section adds in all lengths that are non leaf
+			
+				copyIpcount = copyTree->tree[i].pcount;
+				for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
+					if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+				}
+			
+				//if i's children are from the same group then i's pcount size will be 1 
+				//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
+				if (copyIpcount.size() == 0) { }
+				else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += copyTree->tree[i].getBranchLength();	}
+			
+				//add i's BL to total if it is from the groups the user wants
+				if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
+					totalBL += copyTree->tree[i].getBranchLength(); 
+				}
+			
+				/**********************************************************************/
+				//This section adds in all lengths that are leaf
+			
+				//if i's chidren are leaves
+				if (copyTree->tree[rc].getRChild() == -1) {
+					//if rc is a valid group and rc has a BL
+					if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+						UniqueBL += copyTree->tree[rc].getBranchLength();
+						totalBL += copyTree->tree[rc].getBranchLength(); 
+					}
+				}
+			
+				if (copyTree->tree[lc].getLChild() == -1) {
+					//if lc is a valid group and lc has a BL
+					if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+						UniqueBL += copyTree->tree[lc].getBranchLength();
+						totalBL += copyTree->tree[lc].getBranchLength(); 
+					}
+				}
+			
+				/**********************************************************************/
+			}
+		
+			UW = (UniqueBL / totalBL);  
 	
-		UW /= (UW + shared);
-	
-		if (isnan(UW) || isinf(UW)) { UW = 0; }
+			if (isnan(UW) || isinf(UW)) { UW = 0; }
 	
-		data[0] = UW;
+			data[count] = UW;
+		}
+		
+		delete copyTree;
 		
 		return data;
 	
@@ -82,7 +382,8 @@ EstOutput Unweighted::getValues(Tree* t) {
 		cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}
-
 }
 
-/**************************************************************************************************/
\ No newline at end of file
+
+
+