taxFile = validParameter.validFile(parameters, "taxonomy", true);
if (taxFile == "not open") { taxFile = ""; abort = true; }
else if (taxFile == "not found") { taxFile = ""; }
- else { m->setTaxonomyFile(taxFile); }
+ else { m->setTaxonomyFile(taxFile); if (splitmethod != "fasta") { splitmethod = "classify"; } }
if ((phylipfile == "") && (columnfile == "") && (fastafile == "")) {
//is there are current file available for either of these?
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "splitmethod", false);
- if (splitmethod != "fasta") {
+ if ((splitmethod != "fasta") && (splitmethod != "classify")) {
if (temp == "not found") { splitmethod = "distance"; }
else { splitmethod = temp; }
}
method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "average"; }
- if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
+ if ((method == "furthest") || (method == "nearest") || (method == "average")) { m->mothurOut("Using splitmethod " + splitmethod + ".\n"); }
else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
if ((splitmethod == "distance") || (splitmethod == "classify") || (splitmethod == "fasta")) { }