added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / removegroupscommand.h

diff --git a/removegroupscommand.h b/removegroupscommand.h
index daf2066feade74af3239e12f3a48a7b314de0a4c..103ab66197e7ecd2ea447430a0edfba3eac3c717 100644 (file)
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -35,12 +35,17 @@ public:
        
 private:
        set<string> names;
-       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
        bool abort;
        vector<string> outputNames, Groups;
        GroupMap* groupMap;
+       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
+       
        
        int readFasta();
+       int readShared();
        int readName();
        int readGroup();
        void readAccnos();