changing command name classify.shared to classifyrf.shared

[mothur.git] / parselistscommand.h

diff --git a/parselistscommand.h b/parselistscommand.h
index 8f91017fc6af754030a1940fc818e9d83217e33b..84abc85d46e0bc3fddd916a0095c4b45aa44dbd1 100644 (file)
--- a/parselistscommand.h
+++ b/parselistscommand.h
@@ -19,22 +19,34 @@
 class ParseListCommand : public Command {
        
 public:
-       ParseListCommand(string);       
-       ~ParseListCommand();
-       int execute();  
-       void help();
+       ParseListCommand(string);
+       ParseListCommand();     
+       ~ParseListCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "parse.list";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
+       string getDescription()         { return "parses a list file by group"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void parse(ListVector*);
+       int parse(ListVector*);
                
        ListVector* list;
        GroupMap* groupMap;
-       InputData* input;
+    CountTable ct;
        
        ofstream out;
-       string outputDir, listfile, groupfile, label;
+       string outputDir, listfile, groupfile, label, countfile;
        set<string> labels;
        bool abort, allLines;
+       vector<string> outputNames;
        
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;