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. */
25 class ReadDistCommand : public Command {
27 ReadDistCommand(string);
28 ReadDistCommand() { abort = true; calledHelp = true; }
31 vector<string> setParameters() { return outputNames; } //dummy doesn't really do anything
32 string getCommandName() { return "read.dist"; }
33 string getCommandCategory() { return "Hidden"; }
34 string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; }
35 string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
36 string getDescription() { return "read.dist"; }
39 void help() { m->mothurOut(getHelpString()); }
47 string distFileName, format, method;
48 string phylipfile, columnfile, namefile, groupfile, outputDir;
49 NameAssignment* nameMap;
50 vector<string> outputNames;