added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / splitgroupscommand.h

diff --git a/splitgroupscommand.h b/splitgroupscommand.h
index c45c7ff6b386111ba34897c3e13ff213e832b79f..a8dc9a19e656651be58416c99e802e1b98b72a56 100644 (file)
--- a/splitgroupscommand.h
+++ b/splitgroupscommand.h
@@ -25,25 +25,23 @@ class SplitGroupCommand : public Command {
 public:
        SplitGroupCommand(string);      
        SplitGroupCommand();
-       ~SplitGroupCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~SplitGroupCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "split.group";                         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
+       string getDescription()         { return "split a name or fasta file by group"; }
 
        
-private:
-       int readNames(); 
-       int splitFasta(); 
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
+private:
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-       map<string, vector<string> > nameMap;
-       map<string, vector<string> >::iterator itNames;
-       GroupMap* groupMap;
-       
+               
        string outputDir, namefile, groupfile, groups, fastafile;
        vector<string> Groups;
        bool abort;