added shared file type to get.groups and remove.groups

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 955de627ccb6f4952c6ed3a1444ee2b4d5397187..6d766fb5ebab9f3910e998180bfa92003ca8a68f 100644 (file)
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -26,6 +26,9 @@ public:
        string getCommandName()                 { return "get.groups";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
+       string getDescription()         { return "gets sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -33,7 +36,7 @@ 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;
@@ -45,6 +48,7 @@ private:
        int readList();
        int readTax();
        int fillNames();
+       int readShared();
        
 };