X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=inline;f=unweighted.cpp;h=2a2a41cf0f6b823e3a781d9dabe53702e04d6f78;hb=f07bf12e0d04340698aff7a36d2fee7c959ffe59;hp=b224996efe0bb9a2bbdb517502b93ca6d62e7edf;hpb=99d8e5dde3ee76ae28ead4070d321da195c595c9;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index b224996..2a2a41c 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -15,79 +15,283 @@ EstOutput Unweighted::getValues(Tree* t) {
 	try {
 		globaldata = GlobalData::getInstance();
 		
-		//clear out old values
-		data.resize(1,0); 
-		
-		double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
-		double totalBL = 0.00;	//all branch lengths
-		double UW = 0.00;		//Unweighted Value = UniqueBL / totalBL;
-		
+		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;
+
+	
+		//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);
 		
-		for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+		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]);
 		
-			int lc = t->tree[i].getLChild();  //lc = vector index of left child
-			int rc = t->tree[i].getRChild();  //rc = vector index of right child
+				for(int i=0;i<t->getNumNodes();i++){
+					if (m->control_pressed) {  return data; }
+	
+					copyIpcount = t->tree[i].pcount;
+					for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+						if (inUsersGroups(it->first, groups) != true) {	
+							copyIpcount.erase(it++);	
+						}else { it++;  }
+					}
+			
+					//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 += abs(t->tree[i].getBranchLength());	}
 			
-			/**********************************************************************/
-			//This section adds in all lengths that are non leaf
+					//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 += abs(t->tree[i].getBranchLength()); 
+					}
 			
-			copyIpcount = t->tree[i].pcount;
-			for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
-				if (inUsersGroups(it->first, globaldata->Groups) != true) {	copyIpcount.erase(it->first);	}
+				}
+		
+				UW = (UniqueBL / totalBL);  
+		//cout << globaldata->Groups[a] << globaldata->Groups[l] << '\t' << UniqueBL << '\t' << totalBL << endl;
+	
+				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++) {
+					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]);
+				}
 			}
+		
+			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=0;i<t->getNumNodes();i++){
+			
+				if (m->control_pressed) {  return data; }
+				
+				copyIpcount = t->tree[i].pcount;
+				for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+					if (inUsersGroups(it->first, groups) != true) {	
+						copyIpcount.erase(it++);	
+					}else {  it++;  }
+				}
 			
-			//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();	}
+				//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 += abs(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 += abs(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(); 
 			}
+		
+			UW = (UniqueBL / totalBL);  
+	
+			if (isnan(UW) || isinf(UW)) { UW = 0; }
+	
+			data[count] = UW;
+		}
+
+		return data;
+	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Unweighted", "getValues");
+		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++;
+			}
+		}
+
+		//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]);
+				
+				if (m->control_pressed) { delete copyTree; return data; }
+				
+				//copyTree->createNewickFile("random"+groupA+toString(count));
+				
+				for(int i=0;i<copyTree->getNumNodes();i++){
+					
+					if (m->control_pressed) { delete copyTree; return data; }
+					
+					/**********************************************************************/
+					//This section adds in all lengths that are non leaf
+					copyIpcount = copyTree->tree[i].pcount;
+					for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+						if (inUsersGroups(it->first, groups) != true) {	
+							copyIpcount.erase(it++);	
+						}else { it++;  }
+					}
 			
-			/**********************************************************************/
-			//This section adds in all lengths that are leaf
+					//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 += abs(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 += abs(copyTree->tree[i].getBranchLength()); 
+					}
 			
-			//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(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
-					UniqueBL += t->tree[rc].getBranchLength();
-					totalBL += t->tree[rc].getBranchLength(); 
 				}
+		
+				UW = (UniqueBL / totalBL);  
+	
+				if (isnan(UW) || isinf(UW)) { UW = 0; }
+	
+				data[count] = UW;
+				count++;
+				groups.clear();
 			}
-			
-			if (t->tree[lc].getLChild() == -1) {
-				//if lc is a valid group and lc has a BL
-				if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
-					UniqueBL += t->tree[lc].getBranchLength();
-					totalBL += t->tree[lc].getBranchLength(); 
+		}
+		
+		
+		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]);
 				}
 			}
+		
+			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);
 			
-			/**********************************************************************/
-		}
+			if (m->control_pressed) { delete copyTree; return data; }
+
+			for(int i=0;i<copyTree->getNumNodes();i++){
+				if (m->control_pressed) { delete copyTree; return data; }
+			
+				copyIpcount = copyTree->tree[i].pcount;
+				for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+						if (inUsersGroups(it->first, groups) != true) {	
+							copyIpcount.erase(it++);	
+						}else { it++;  }
+				}
+			
+				//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)) {  abs(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 += abs(copyTree->tree[i].getBranchLength()); 
+				}
+			
+			}
 		
-		UW = (UniqueBL / totalBL);  
+			UW = (UniqueBL / totalBL);  
 	
-		if (isnan(UW) || isinf(UW)) { UW = 0; }
+			if (isnan(UW) || isinf(UW)) { UW = 0; }
 	
-		data[0] = UW;
+			data[count] = UW;
+		}
+		
+		delete copyTree;
 		
 		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";
+		m->errorOut(e, "Unweighted", "getValues");
 		exit(1);
 	}
-
 }
 
+
+
+