If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed. */
class NameAssignment;
-class GlobalData;
-
class ReadDistCommand : public Command {
public:
ReadDistCommand(string);
- ReadDistCommand() {}
- ~ReadDistCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ReadDistCommand() { abort = true; calledHelp = true; }
+ ~ReadDistCommand() {}
+
+ vector<string> setParameters() { return outputNames; } //dummy doesn't really do anything
+ string getCommandName() { return "read.dist"; }
+ string getCommandCategory() { return "Hidden"; }
+ string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; }
+ string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
double cutoff;
int precision;
ReadMatrix* read;
string phylipfile, columnfile, namefile, groupfile, outputDir;
NameAssignment* nameMap;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
bool abort, sim;