From: westcott <westcott>
Date: Mon, 9 Mar 2009 19:03:35 +0000 (+0000)
Subject: added abs() to weighted and unweighted to account for negative branch lengths
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=503b23b959230453d95dc812fbbe088b3be6910c

added abs() to weighted and unweighted to account for negative branch lengths
---

diff --git a/unweighted.cpp b/unweighted.cpp
index 405dfd2..3694d26 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()); 
 						}
 					}
 			
@@ -138,11 +138,11 @@ 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 +152,16 @@ 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()); 
 					}
 				}
 			
@@ -252,11 +252,11 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 					//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()); 
 					}
 			
 					/**********************************************************************/
@@ -266,16 +266,16 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 					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(); 
+							UniqueBL += abs(copyTree->tree[rc].getBranchLength());
+							totalBL += abs(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(); 
+							UniqueBL += abs(copyTree->tree[lc].getBranchLength());
+							totalBL += abs(copyTree->tree[lc].getBranchLength()); 
 						}
 					}
 			
@@ -332,11 +332,11 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 				//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()); 
 				}
 			
 				/**********************************************************************/
@@ -346,16 +346,16 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 				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(); 
+						UniqueBL += abs(copyTree->tree[rc].getBranchLength());
+						totalBL += abs(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(); 
+						UniqueBL += abs(copyTree->tree[lc].getBranchLength());
+						totalBL += abs(copyTree->tree[lc].getBranchLength()); 
 					}
 				}
 			
diff --git a/weighted.cpp b/weighted.cpp
index fa22716..5810780 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -39,14 +39,14 @@ EstOutput Weighted::getValues(Tree* t) {
 							
 						//if you have a BL
 						if(t->tree[index].getBranchLength() != -1){
-							sum += t->tree[index].getBranchLength();
+							sum += abs(t->tree[index].getBranchLength());
 						}
 						index = t->tree[index].getParent();
 					}
 						
 					//get last breanch length added
 					if(t->tree[index].getBranchLength() != -1){
-						sum += t->tree[index].getBranchLength();
+						sum += abs(t->tree[index].getBranchLength());
 					}
 						
 					//is this sum from a sequence which is in one of the users groups
@@ -85,7 +85,7 @@ EstOutput Weighted::getValues(Tree* t) {
 						u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
 					}
 						
-					u = abs(u) * t->tree[i].getBranchLength();
+					u = abs(u * t->tree[i].getBranchLength());
 					
 					//save groupcombs u value
 					WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
@@ -142,14 +142,14 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 							
 				//if you have a BL
 				if(t->tree[index].getBranchLength() != -1){
-					sum += t->tree[index].getBranchLength();
+					sum += abs(t->tree[index].getBranchLength());
 				}
 				index = t->tree[index].getParent();
 			}
 						
 			//get last breanch length added
 			if(t->tree[index].getBranchLength() != -1){
-				sum += t->tree[index].getBranchLength();
+				sum += abs(t->tree[index].getBranchLength());
 			}
 						
 			if ((t->tree[v].getGroup() == groupA) || (t->tree[v].getGroup() == groupB)) {
@@ -177,7 +177,7 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
 				u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
 			}
 						
-			u = abs(u) * t->tree[i].getBranchLength();
+			u = abs(u * t->tree[i].getBranchLength());
 					
 			//save groupcombs u value
 			WScore[(groupA+groupB)] += u;