added name, group and count files to chop.seqs. added intelligent warnings for when...

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index e5d8427200aed0a61aaf04a0e7084ed0e17a0a78..8e2139db771010d1b372ccfdc0a6a0523c6e4849 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -317,6 +317,10 @@ string GroupMap::getGroup(string sequenceName) {
        if (it != groupmap.end()) { //sequence name was in group file
                return it->second;      
        }else {
+        //look for it in names of groups to see if the user accidently used the wrong file
+        if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+            m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine(); 
+        }
                return "not found";
        }
 }