*/
#include "command.hpp"
-#include "globaldata.hpp"
/*
Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
public:
ClearcutCommand(string);
ClearcutCommand();
- ~ClearcutCommand() {};
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ClearcutCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "clearcut"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
+ string getDescription() { return "create a tree from a fasta or phylip file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
bool abort;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
+
};
/****************************************************************************/