sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / parselistscommand.h

diff --git a/parselistscommand.h b/parselistscommand.h
index 5ecc7ab13205d4f34d7c496a6b2cc3221615eafe..84abc85d46e0bc3fddd916a0095c4b45aa44dbd1 100644 (file)
--- a/parselistscommand.h
+++ b/parselistscommand.h
@@ -21,27 +21,32 @@ class ParseListCommand : public Command {
 public:
        ParseListCommand(string);
        ParseListCommand();     
-       ~ParseListCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~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:
        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, vector<string> > outputTypes;
        
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;