changes while testing

[mothur.git] / mergegroupscommand.h

diff --git a/mergegroupscommand.h b/mergegroupscommand.h
index 62839ec1a1dc80a3b77a7aad8666f35262f663b3..3e3d337ffa0309f5132d2d88cc3b4c0b81684869 100644 (file)
--- a/mergegroupscommand.h
+++ b/mergegroupscommand.h
@@ -14,33 +14,38 @@
 #include "inputdata.h"
 #include "sharedrabundvector.h"
 
-class GlobalData;
-
 class MergeGroupsCommand : public Command {
        
 public:
        MergeGroupsCommand(string);
        MergeGroupsCommand();
-       ~MergeGroupsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~MergeGroupsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "merge.groups";        }
+       string getCommandCategory()             { return "General";                     }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
+       string getDescription()         { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        GroupMap* designMap;
        vector<SharedRAbundVector*> lookup;
-       map<string, vector<string> > outputTypes;
        
        bool abort, allLines, pickedGroups;
        set<string> labels; //holds labels to be used
-       string groups, label, outputDir, inputDir, designfile, sharedfile;
+       string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
        vector<string> Groups, outputNames;
                
        int process(vector<SharedRAbundVector*>&, ofstream&);
+       int processSharedFile(GroupMap*&);
+       int processGroupFile(GroupMap*&);
 };
 
 #endif