X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=687786a71e783bdb4df476eb17d6864e07238974;hb=6e63c5ff52bd2830b689417df8ba3db831e63a96;hp=16a2203274f325ffc8d8b5febfea903597340093;hpb=38922fcff5a03abfedffda3e06a45fad2270a044;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index 16a2203..687786a 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -64,11 +64,11 @@ EstOutput Unweighted::getValues(Tree* t) {
 					//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();	}
+					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 += t->tree[i].getBranchLength(); 
+						totalBL += abs(t->tree[i].getBranchLength()); 
 					}
 			
 					/**********************************************************************/
@@ -78,16 +78,16 @@ EstOutput Unweighted::getValues(Tree* t) {
 					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(); 
+							UniqueBL += abs(t->tree[rc].getBranchLength());
+							totalBL += abs(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(); 
+							UniqueBL += abs(t->tree[lc].getBranchLength());
+							totalBL += abs(t->tree[lc].getBranchLength()); 
 						}
 					}
 			
@@ -109,7 +109,9 @@ EstOutput Unweighted::getValues(Tree* t) {
 			if (numGroups == 0) {
 				//get score for all users groups
 				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-					groups.push_back(tmap->namesOfGroups[i]);
+					if (tmap->namesOfGroups[i] != "xxx") {
+						groups.push_back(tmap->namesOfGroups[i]);
+					}
 				}
 			}else {
 				for (int i = 0; i < globaldata->Groups.size(); i++) {
@@ -138,11 +140,11 @@ EstOutput Unweighted::getValues(Tree* t) {
 				//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();	}
+				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 += t->tree[i].getBranchLength(); 
+					totalBL += abs(t->tree[i].getBranchLength()); 
 				}
 			
 				/**********************************************************************/
@@ -152,16 +154,16 @@ EstOutput Unweighted::getValues(Tree* t) {
 				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(); 
+						UniqueBL += abs(t->tree[rc].getBranchLength());
+						totalBL += abs(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(); 
+						UniqueBL += abs(t->tree[lc].getBranchLength());
+						totalBL += abs(t->tree[lc].getBranchLength()); 
 					}
 				}
 			
@@ -179,14 +181,9 @@ EstOutput Unweighted::getValues(Tree* t) {
 	
 	}
 	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";
+		errorOut(e, "Unweighted", "getValues");
 		exit(1);
 	}
-
 }
 
 /**************************************************************************************************/
@@ -205,7 +202,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 
 		//if the users enters no groups then give them the score of all groups
 		int numGroups = globaldata->Groups.size();
-cout << "NumGroups = " << numGroups << endl;
+
 		//calculate number of comparsions
 		int numComp = 0;
 		for (int r=0; r<numGroups; r++) { 
@@ -233,17 +230,18 @@ cout << "NumGroups = " << numGroups << endl;
 				
 				//swap labels in the groups you want to compare
 				copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
-
+				
+				//copyTree->createNewickFile("random"+groupA+toString(count));
 		
-				for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+				for(int i=copyTree->getNumLeaves();i<copyTree->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 = 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 = t->tree[i].pcount;
+					copyIpcount = copyTree->tree[i].pcount;
 					for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 						if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
 					}
@@ -251,30 +249,30 @@ cout << "NumGroups = " << numGroups << endl;
 					//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();	}
+					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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
-						totalBL += t->tree[i].getBranchLength(); 
+					if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
+						totalBL += abs(copyTree->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 (copyTree->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 ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+							UniqueBL += abs(copyTree->tree[rc].getBranchLength());
+							totalBL += abs(copyTree->tree[rc].getBranchLength()); 
 						}
 					}
 			
-					if (t->tree[lc].getLChild() == -1) {
+					if (copyTree->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(); 
+						if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+							UniqueBL += abs(copyTree->tree[lc].getBranchLength());
+							totalBL += abs(copyTree->tree[lc].getBranchLength()); 
 						}
 					}
 			
@@ -296,7 +294,9 @@ cout << "NumGroups = " << numGroups << endl;
 			if (numGroups == 0) {
 				//get score for all users groups
 				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-					groups.push_back(tmap->namesOfGroups[i]);
+					if (tmap->namesOfGroups[i] != "xxx") {
+						groups.push_back(tmap->namesOfGroups[i]);
+					}
 				}
 			}else {
 				for (int i = 0; i < globaldata->Groups.size(); i++) {
@@ -315,15 +315,15 @@ cout << "NumGroups = " << numGroups << endl;
 			//swap labels in all the groups you want to compare
 			copyTree->assembleRandomUnifracTree(groups);
 
-			for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+			for(int i=copyTree->getNumLeaves();i<copyTree->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 = 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 = t->tree[i].pcount;
+				copyIpcount = copyTree->tree[i].pcount;
 				for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 					if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
 				}
@@ -331,30 +331,30 @@ cout << "NumGroups = " << numGroups << endl;
 				//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();	}
+				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 ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
-					totalBL += t->tree[i].getBranchLength(); 
+				if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
+					totalBL += abs(copyTree->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 (copyTree->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 ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+						UniqueBL += abs(copyTree->tree[rc].getBranchLength());
+						totalBL += abs(copyTree->tree[rc].getBranchLength()); 
 					}
 				}
 			
-				if (t->tree[lc].getLChild() == -1) {
+				if (copyTree->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(); 
+					if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+						UniqueBL += abs(copyTree->tree[lc].getBranchLength());
+						totalBL += abs(copyTree->tree[lc].getBranchLength()); 
 					}
 				}
 			
@@ -367,16 +367,14 @@ cout << "NumGroups = " << numGroups << endl;
 	
 			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";
+		errorOut(e, "Unweighted", "getValues");
 		exit(1);
 	}
 }