fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / treemap.cpp

diff --git a/treemap.cpp b/treemap.cpp
index 6314eb04d04006ba5c57808f6927bddec89d6a00..fee309c5877138039c2ecdff8f54428a8060bc24 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -47,7 +47,7 @@ void TreeMap::readMap() {
 
 int TreeMap::getNumGroups() {
                        
-       return seqsPerGroup.size();     
+       return namesOfGroups.size();    
                
 }
 /************************************************************/
@@ -72,7 +72,13 @@ string TreeMap::getGroup(string sequenceName) {
 }
 /************************************************************/
 void TreeMap::setIndex(string seq, int index) {
-       treemap[seq].vectorIndex = index;
+       it = treemap.find(seq);
+       if (it != treemap.end()) { //sequence name was in group file
+               treemap[seq].vectorIndex = index;       
+       }else {
+               treemap[seq].vectorIndex = index;
+               treemap[seq].groupname = "not found";
+       }
 }
 /************************************************************/
 int TreeMap::getIndex(string seq) {