X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=84b0861e38cc450b50b481e7efdaaa76e0831e4e;hb=7837a9bfdfccdc26360987a44c389832fdb82651;hp=915a05ff74a14e7fac2a32da119c184ee9908293;hpb=89d6711c2beed6ee75fb00e5e57f1a91564d3e89;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 915a05f..84b0861 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -114,6 +114,8 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 					//find out the sequences group
 					string group = groupmap->getGroup(seqName);
 					
+					if (group == "not found") {  m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine();  }
+					
 					//do you have a count for this group?
 					map<string, int>::iterator itGroup = tree[currentNode].groupCount.find(group);
 					
@@ -177,8 +179,15 @@ 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) {
@@ -206,7 +215,15 @@ 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) {