Revert to previous commit

[mothur.git] / source / readdistcommand.h

diff --git a/source/readdistcommand.h b/source/readdistcommand.h
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-#ifndef READDISTCOMMAND_H
-#define READDISTCOMMAND_H
-/*
- *  readdistcommand.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 1/20/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "readmatrix.hpp"
-#include "fullmatrix.h"
-#include "groupmap.h"
-
-/* The read.dist command is used to read a distance matrix file.  
-The read.dist command parameter options are phylipfile, columnfile, namefile, cutoff and precision. 
-The read.dist command should be in the following format: read.dist(phylipfile=yourDistFile, 
-namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision). The phylipfile or columnfile are required and if you use a columnfile the namefile is required.  
-If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.  */
-
-class NameAssignment;
-
-class ReadDistCommand : public Command {
-public:
-       ReadDistCommand(string);
-       ReadDistCommand() { abort = true; calledHelp = true; }
-       ~ReadDistCommand() {}
-       
-       vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
-       string getCommandName()                 { return "read.dist";   }
-       string getCommandCategory()             { return "Hidden";      }
-       string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; } 
-       string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
-       string getDescription()         { return "read.dist"; }
-
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       double cutoff;
-       int precision;
-       ReadMatrix* read;
-       FullMatrix* matrix;
-       GroupMap* groupMap;
-       string distFileName, format, method;
-       string phylipfile, columnfile, namefile, groupfile, outputDir;
-       NameAssignment* nameMap;
-       vector<string> outputNames;
-
-       bool abort, sim;
-
-};
-
-#endif