X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistcommand.h;h=afe077d4e0e16c7763dc8304130242d2e0af1d4e;hb=e98d56be8369a799e61a411bc13d3bd1fa3451e5;hp=b6e3ae44de298a115ce9a72de193b51ff951ea34;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/readdistcommand.h b/readdistcommand.h
index b6e3ae4..afe077d 100644
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -21,30 +21,35 @@ 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(string);
-	~ReadDistCommand();
-	int execute();
-	void help();
+	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;
 	FullMatrix* matrix;
 	GroupMap* groupMap;
-	string filename, format, method;
-	string phylipfile, columnfile, namefile, groupfile;
+	string distFileName, format, method;
+	string phylipfile, columnfile, namefile, groupfile, outputDir;
 	NameAssignment* nameMap;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort;
+	vector<string> outputNames;
+
+	bool abort, sim;
 
 };