changing command name classify.shared to classifyrf.shared

[mothur.git] / getsharedotucommand.h

diff --git a/getsharedotucommand.h b/getsharedotucommand.h
index d7ffef3c74b965967dd6f68d7a6914183ec2253f..f03b5ddcf6b5de00eba42210d39c74e46848d73c 100644 (file)
--- a/getsharedotucommand.h
+++ b/getsharedotucommand.h
@@ -14,6 +14,8 @@
 #include "listvector.hpp"
 #include "sequence.hpp"
 #include "groupmap.h"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
 
 //**********************************************************************************************************************
 class GetSharedOTUCommand : public Command {
@@ -28,9 +30,12 @@ class GetSharedOTUCommand : public Command {
                string getCommandName()                 { return "get.sharedseqs";                      }
                string getCommandCategory()             { return "OTU-Based Approaches";        }
                string getRequiredCommand()             { return "none";                                        }
-               string getHelpString(); 
+               
+       string getHelpString(); 
+    string getOutputPattern(string);   
                string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
-       
+               string getDescription()         { return "identifies sequences that are either unique or shared by specific groups"; }
+
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  
        
@@ -41,7 +46,7 @@ class GetSharedOTUCommand : public Command {
                GroupMap* groupMap;
                
                set<string> labels;
-               string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir, format;
+               string fastafile, label, groups, listfile, groupfile, sharedfile, output, userGroups, outputDir, format;
                bool abort, allLines, unique;
                vector<string> Groups;
                map<string, string> groupFinder;
@@ -50,6 +55,8 @@ class GetSharedOTUCommand : public Command {
                vector<string> outputNames;
                
                int process(ListVector*);
+        int process(vector<SharedRAbundVector*>&);
+        int runShared();
                
 };
 //**********************************************************************************************************************