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

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 5612d7bbf3eded6f86bcdce40c45048ee8edcb25..33396975f506626ff275a8c37fa6c0f83a3ead18 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -172,6 +172,9 @@ void PhyloSummary::print(ofstream& out){
                //print labels
                out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
                if (groupmap != NULL) {
+                       //so the labels match the counts below, since the map sorts them automatically...
+                       //sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
+                       
                        for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
                                out << groupmap->namesOfGroups[i] << '\t';
                        }
@@ -179,14 +182,22 @@ void PhyloSummary::print(ofstream& out){
                
                out << endl;
                
+               int totalChildrenInTree = 0;
+               
+               map<string,int>::iterator it;
+               for(it=tree[0].children.begin();it!=tree[0].children.end();it++){   
+                       if (tree[it->second].total != 0)  {   totalChildrenInTree++; }
+               }
+               
                //print root
-               out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << tree[0].children.size() << "\t" << tree[0].total << "\t";
+               out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
                
                map<string, int>::iterator itGroup;
                if (groupmap != NULL) {
-                       for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
-                               out << itGroup->second << '\t';
-                       }
+                       //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
+                       //      out << itGroup->second << '\t';
+                       //}
+                       for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[0].groupCount[groupmap->namesOfGroups[i]] << '\t'; } 
                }
                out << endl;
                
@@ -208,13 +219,22 @@ void PhyloSummary::print(int i, ofstream& out){
                for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
                        
                        if (tree[it->second].total != 0)  {
-                               out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << tree[it->second].children.size() << "\t" << tree[it->second].total << "\t";
+                       
+                               int totalChildrenInTree = 0;
+               
+                               map<string,int>::iterator it2;
+                               for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){   
+                                       if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
+                               }
+                       
+                               out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
                                
                                map<string, int>::iterator itGroup;
                                if (groupmap != NULL) {
-                                       for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
-                                               out << itGroup->second << '\t';
-                                       }
+                                       //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
+                                       //      out << itGroup->second << '\t';
+                                       //}
+                                       for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[it->second].groupCount[groupmap->namesOfGroups[i]] << '\t'; } 
                                }
                                out << endl;
                        }