*/
#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();
private:
string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
- bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdout, kimura, jukes, protein, DNA, stdin;
+ bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
bool abort;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
};
/****************************************************************************/