X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistcommand.h;h=afe077d4e0e16c7763dc8304130242d2e0af1d4e;hb=133dddf9ffde5059e3ea8290a2e7742843e3f2b7;hp=4f38d034f1f14e320da5495ac79a04d4deff16b3;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/readdistcommand.h b/readdistcommand.h
index 4f38d03..afe077d 100644
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -9,10 +9,10 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #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. 
@@ -21,22 +21,36 @@ namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision). The phylipfi
 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 GlobalData;
-
 
 class ReadDistCommand : public Command {
 public:
-	ReadDistCommand();
-	~ReadDistCommand();
-	int execute();
+	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:
-	GlobalData* globaldata;
 	double cutoff;
 	int precision;
 	ReadMatrix* read;
-	string filename, format, method;
+	FullMatrix* matrix;
+	GroupMap* groupMap;
+	string distFileName, format, method;
+	string phylipfile, columnfile, namefile, groupfile, outputDir;
 	NameAssignment* nameMap;
+	vector<string> outputNames;
+
+	bool abort, sim;
+
 };
 
 #endif