finished shhh.seqs command, fixed bug with remove.groups and get.groups that caused...

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 6d766fb5ebab9f3910e998180bfa92003ca8a68f..e0fbad80064157e99c3ff21fb97ddfd95bc97317 100644 (file)
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -36,6 +36,9 @@ public:
        
 private:
        set<string> names;
+       map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+                                                                                  //then the other files need to change the unique name in their file to match.
+                                                                                  //only add the names that need to be changed to keep the map search quick
        string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
        bool abort;
        vector<string> outputNames, Groups;