1 #ifndef CLEARCUTCOMMAND_H
2 #define CLEARCUTCOMMAND_H
8 * Created by westcott on 5/11/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "globaldata.hpp"
17 Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
18 A Fast Distance-Based Phylogenetic Tree Construction Method,
19 J. Mol. Evol., 62, 785-792
22 /****************************************************************************/
24 class ClearcutCommand : public Command {
27 ClearcutCommand(string);
29 ~ClearcutCommand() {};
30 vector<string> getRequiredParameters();
31 vector<string> getValidParameters();
32 vector<string> getRequiredFiles();
33 map<string, vector<string> > getOutputFiles() { return outputTypes; }
38 string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
39 bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
41 vector<string> outputNames;
42 map<string, vector<string> > outputTypes;
45 /****************************************************************************/