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:
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;