+//**********************************************************************************************************************
+
+void ReadDistCommand::help(){
+ try {
+ cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
+ cout << "The read.dist command can be used in two ways. The first is to read a phylip or column and run the cluster command" << "\n";
+ cout << "For this use the read.dist command should be in the following format: " << "\n";
+ cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
+ cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n";
+ cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n";
+ cout << "The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command." << "\n";
+ cout << "For this use the read.dist command should be in the following format: " << "\n";
+ cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. " << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadDistCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}