///variables for examples below that you will most likely want to put in the header for
//use by the other class functions.
- string phylipfile, columnfile, namefile, fastafile, sharedfile, method;
+ string phylipfile, columnfile, namefile, fastafile, sharedfile, method, countfile;
int processors;
bool useTiming, allLines;
vector<string> Estimators, Groups;
//saved by mothur that is associated with the other files you are using as inputs.
//You can do so by adding the files associated with the namefile to the files vector and then asking parser to check.
//This saves our users headaches over file mismatches because they forgot to include the namefile, :)
- if (namefile == "") {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
+
}