public:
DistanceCommand(string);
DistanceCommand();
- ~DistanceCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~DistanceCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "dist.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
struct distlinePair {
bool abort;
vector<string> Estimators, outputNames; //holds estimators to be used
- map<string, vector<string> > outputTypes;
//void m->appendFiles(string, string);
void createProcesses(string);