#include "readtree.h"
#include "treemap.h"
-class GlobalData;
class ReadTreeCommand : public Command {
public:
ReadTreeCommand(string);
- ~ReadTreeCommand();
- int execute();
- void help();
+ ReadTreeCommand() { abort = true; calledHelp = true; }
+ ~ReadTreeCommand() {}
+
+ vector<string> setParameters() { return outputNames; } //dummy doesn't really do anything
+ string getCommandName() { return "read.tree"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like unifrac.unweighted."; }
+ string getCitation() { return "http://www.mothur.org/wiki/Read.tree"; }
+ string getDescription() { return "read.tree"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
ReadTree* read;
TreeMap* treeMap;
string filename, treefile, groupfile, namefile;
bool abort;
map<string, string> nameMap;
+ vector<string> outputNames;
int readNamesFile();
+ int numUniquesInName;
};