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

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 642107dafc9d567aa93270195740030d33698e52..e0fbad80064157e99c3ff21fb97ddfd95bc97317 100644 (file)
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -36,7 +36,10 @@ public:
        
 private:
        set<string> names;
-       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+       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;
        GroupMap* groupMap;
@@ -48,6 +51,7 @@ private:
        int readList();
        int readTax();
        int fillNames();
+       int readShared();
        
 };