1 #ifndef READDISTCOMMAND_H
2 #define READDISTCOMMAND_H
7 * Created by Sarah Westcott on 1/20/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "readmatrix.hpp"
14 #include "fullmatrix.h"
17 /* The read.dist command is used to read a distance matrix file.
18 The read.dist command parameter options are phylipfile, columnfile, namefile, cutoff and precision.
19 The read.dist command should be in the following format: read.dist(phylipfile=yourDistFile,
20 namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision). The phylipfile or columnfile are required and if you use a columnfile the namefile is required.
21 If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed. */
27 class ReadDistCommand : public Command {
29 ReadDistCommand(string);
35 GlobalData* globaldata;
41 string distFileName, format, method;
42 string phylipfile, columnfile, namefile, groupfile, outputDir;
43 NameAssignment* nameMap;
45 bool abort, sim, hard;