fixed bug with phylo.diversity. not calculating as intended.

[mothur.git] / phylodiversity.cpp

diff --git a/phylodiversity.cpp b/phylodiversity.cpp
index 37884c483619887bcc478b6fdf7e77be08424cd4..86dc539b8e1a6e1385d178ab0473bcc966a71705 100644 (file)
--- 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);
-       }
-}
-/**************************************************************************************************/