X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversity.cpp;h=86dc539b8e1a6e1385d178ab0473bcc966a71705;hb=515c3398ea27e2105f616fc5662b2a7ceb486aa0;hp=37884c483619887bcc478b6fdf7e77be08424cd4;hpb=0b99c6b6ea875e13febda76903fd4d9cda7add7d;p=mothur.git

diff --git a/phylodiversity.cpp b/phylodiversity.cpp
index 37884c4..86dc539 100644
--- a/phylodiversity.cpp
+++ b/phylodiversity.cpp
@@ -9,8 +9,8 @@
 
 #include "phylodiversity.h"
 
-/**************************************************************************************************/
-EstOutput PhyloDiversity::getValues(Tree* t, vector<int> treeNodes) {
+/**************************************************************************************************
+EstOutput PhyloDiversity::getValues(Tree* t, vector<int> treeNodes, vector< vector<float> >& data) {
     try {
 		
 		map<string, float> DScore;
@@ -20,57 +20,52 @@ EstOutput PhyloDiversity::getValues(Tree* t, vector<int> treeNodes) {
 		//initialize Dscore
 		for (int i=0; i<globaldata->Groups.size(); i++) {		DScore[globaldata->Groups[i]] = 0.0;	}
 	
-		/********************************************************/
+		/********************************************************
 		//calculate a D value for each group 
 		for(int v=0;v<treeNodes.size();v++){
 				
 			if (m->control_pressed) { return data; }
 			
-			//is this node from a sequence which is in one of the users groups
-			if (inUsersGroups(t->tree[treeNodes[v]].getGroup(), globaldata->Groups) == true) {
-					
-				//calc the branch length
-				//while you aren't at root
-				float sum = 0.0;
-				int index = treeNodes[v];
+			//calc the branch length
+			//while you aren't at root
+			float sum = 0.0;
+			int index = treeNodes[v];
 
-				while(t->tree[index].getParent() != -1){
-					
-					//if you have a BL
-					if(t->tree[index].getBranchLength() != -1){
-						sum += abs(t->tree[index].getBranchLength());
-					}
-					index = t->tree[index].getParent();
-				}
-					
-				//get last breanch length added
+			while(t->tree[index].getParent() != -1){
+				
+				//if you have a BL
 				if(t->tree[index].getBranchLength() != -1){
 					sum += abs(t->tree[index].getBranchLength());
 				}
-					
-				//for each group in the groups update the total branch length accounting for the names file
-				vector<string> groups = t->tree[treeNodes[v]].getGroup();
-				for (int j = 0; j < groups.size(); j++) {
-					int numSeqsInGroupJ = 0;
-					map<string, int>::iterator it;
-					it = t->tree[treeNodes[v]].pcount.find(groups[j]);
-					if (it != t->tree[treeNodes[v]].pcount.end()) { //this leaf node contains seqs from group j
-						numSeqsInGroupJ = it->second;
-					}
-
-					//add branch length to total for group
-					DScore[groups[j]] += (numSeqsInGroupJ * sum);
+				index = t->tree[index].getParent();
+			}
+				
+			//get last breanch length added
+			if(t->tree[index].getBranchLength() != -1){
+				sum += abs(t->tree[index].getBranchLength());
+			}
+				
+			//for each group in the groups update the total branch length accounting for the names file
+			vector<string> groups = t->tree[treeNodes[v]].getGroup();
+			for (int j = 0; j < groups.size(); j++) {
+				int numSeqsInGroupJ = 0;
+				map<string, int>::iterator it;
+				it = t->tree[treeNodes[v]].pcount.find(groups[j]);
+				if (it != t->tree[treeNodes[v]].pcount.end()) { //this leaf node contains seqs from group j
+					numSeqsInGroupJ = it->second;
 				}
+
+				//add branch length to total for group
+				DScore[groups[j]] += (numSeqsInGroupJ * sum);
 			}
+			
 		}
 		
 	
 		for (int i=0; i<globaldata->Groups.size(); i++) {   
-			//if (groupTotals[globaldata->Groups[i]] != 0.0) { //avoid divide by zero error
-				//float percent = DScore[globaldata->Groups[i]] / groupTotals[globaldata->Groups[i]];
 			float percent = DScore[globaldata->Groups[i]]; 
 			data.push_back(percent);  
-			//}else {  data.push_back(0.0);  }
+			
 		}
 		
 		return data;
@@ -81,62 +76,6 @@ EstOutput PhyloDiversity::getValues(Tree* t, vector<int> treeNodes) {
 	}
 }
 /**************************************************************************************************/
-void PhyloDiversity::setTotalGroupBranchLengths(Tree* t) {
-    try {
-		
-		groupTotals.clear();
-		
-		//initialize group totals
-		for (int i=0; i<globaldata->Groups.size(); i++) {		groupTotals[globaldata->Groups[i]] = 0.0;	}
-		
-		
-		/********************************************************/
-		//calculate a D value for each group 
-		for(int v=0;v<t->getNumLeaves();v++){
-			
-			//is this node from a sequence which is in one of the users groups
-			if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
-			
-				//calc the branch length
-				int index = v;
-				float sum = 0.0;
-				
-				while(t->tree[index].getParent() != -1){  //while you aren't at root
-						
-					//if you have a BL
-					if(t->tree[index].getBranchLength() != -1){
-						sum += abs(t->tree[index].getBranchLength());
-					}
-					index = t->tree[index].getParent();
-				}
-					
-				//get last breanch length added
-				if(t->tree[index].getBranchLength() != -1){
-					sum += abs(t->tree[index].getBranchLength());
-				}
-							
-				//account for the names file
-				vector<string> groups = t->tree[v].getGroup();
-				for (int j = 0; j < groups.size(); j++) {
-					int numSeqsInGroupJ = 0;
-					map<string, int>::iterator it;
-					it = t->tree[v].pcount.find(groups[j]);
-					if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group j
-						numSeqsInGroupJ = it->second;
-					}
 
-					//add branch length to total for group
-					groupTotals[groups[j]] += (numSeqsInGroupJ * sum);
-				}//end for
-			}//end if
-		}//end for
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloDiversity", "setTotalGroupBranchLengths");
-		exit(1);
-	}
-}
-/**************************************************************************************************/