method = validParameter.validFile(parameters, "method", false);
if (method == "not found") { method = "furthest"; }
- if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
- else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
+ if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
+ else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average or weighted."); m->mothurOutEndLine(); abort = true; }
showabund = validParameter.validFile(parameters, "showabund", false);
if (showabund == "not found") { showabund = "T"; }
if (method == "furthest") { tag = "fn"; }
else if (method == "nearest") { tag = "nn"; }
+ else if (method == "weighted") { tag = "wn"; }
else { tag = "an"; }
m->openOutputFile(fileroot+ tag + ".sabund", sabundFile);
m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
m->mothurOut("The hcluster command should be in the following format: \n");
m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- m->mothurOut("The acceptable hcluster methods are furthest, nearest and average.\n\n");
+ m->mothurOut("The acceptable hcluster methods are furthest, nearest, weighted and average.\n\n");
}
catch(exception& e) {
m->errorOut(e, "HClusterCommand", "help");