X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.cpp;h=2a2a41cf0f6b823e3a781d9dabe53702e04d6f78;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=405dfd2b3feaf4c1a5327526936a7baaaa4aba0a;hpb=8fd4a602269974e6548f4a387dddd6bd80a999ab;p=mothur.git

diff --git a/unweighted.cpp b/unweighted.cpp
index 405dfd2..2a2a41c 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -48,53 +48,30 @@ EstOutput Unweighted::getValues(Tree* t) {
 				//groups in this combo
 				groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 		
-				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
-			
+				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(); it++) {
-						if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+					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();	}
+					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(); 
-					}
-			
-					/**********************************************************************/
-					//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(); 
-						}
+						totalBL += abs(t->tree[i].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);  
+		//cout << globaldata->Groups[a] << globaldata->Groups[l] << '\t' << UniqueBL << '\t' << totalBL << endl;
 	
 				if (isnan(UW) || isinf(UW)) { UW = 0; }
 	
@@ -109,7 +86,9 @@ 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++) {
@@ -122,50 +101,27 @@ EstOutput Unweighted::getValues(Tree* t) {
 			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
+			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(); it++) {
-					if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+				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();	}
+				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(); 
-				}
-			
-				/**********************************************************************/
-				//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(); 
-					}
+					totalBL += abs(t->tree[i].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);  
@@ -179,14 +135,9 @@ 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";
+		m->errorOut(e, "Unweighted", "getValues");
 		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);
-	}
-
 }
 
 /**************************************************************************************************/
@@ -234,52 +185,33 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 				//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=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
-			
+				
+				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(); it++) {
-						if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+					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)) {  UniqueBL += copyTree->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 ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
-						totalBL += copyTree->tree[i].getBranchLength(); 
+						totalBL += abs(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);  
@@ -297,7 +229,9 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 			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++) {
@@ -315,51 +249,29 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 				
 			//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
+			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(); it++) {
-					if (inUsersGroups(it->first, groups) != true) {	copyIpcount.erase(it->first);	}
+				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)) {  UniqueBL += copyTree->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 ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {  
-					totalBL += copyTree->tree[i].getBranchLength(); 
+					totalBL += abs(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);  
@@ -375,11 +287,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 	
 	}
 	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);
 	}
 }