added count.groups command and paralellized align.seqs for windows

[mothur.git] / splitgroupscommand.h

diff --git a/splitgroupscommand.h b/splitgroupscommand.h
index c45c7ff6b386111ba34897c3e13ff213e832b79f..f8bdca17e2a06877a81d4d5eca2fcabd64cef52a 100644 (file)
--- a/splitgroupscommand.h
+++ b/splitgroupscommand.h
@@ -25,21 +25,24 @@ 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 getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
+       string getDescription()         { return "split a name or fasta file by group"; }
 
        
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
 private:
        int readNames(); 
        int splitFasta(); 
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        map<string, vector<string> > nameMap;
        map<string, vector<string> >::iterator itNames;
        GroupMap* groupMap;