phylipFileName = validParameter.validFile(parameters, "phylip", true);
if (phylipFileName == "not open") { phylipFileName = ""; abort = true; }
- else if (phylipFileName == "not found") { phylipFileName = ""; }
- else if (designFileName == "not found") {
- designFileName = "";
- m->mothurOut("You must provide an phylip file.");
- m->mothurOutEndLine();
- abort = true;
+ else if (phylipFileName == "not found") {
+ phylipFileName = "";
+
+ //check currentFiles for a phylip file
+ if (currentFiles->getPhylipFile() != "") { phylipFileName = currentFiles->getPhylipFile(); m->mothurOut("Using " + phylipFileName + " as phylip file."); m->mothurOutEndLine();
+ }else { m->mothurOut("You must provide an phylip file."); m->mothurOutEndLine(); abort = true; }
}
//check for required parameters
if (designFileName == "not open") { abort = true; }
else if (designFileName == "not found") {
designFileName = "";
- m->mothurOut("You must provide an design file.");
- m->mothurOutEndLine();
- abort = true;
+
+ //check currentFiles for a design file
+ if (currentFiles->getDesignFile() != "") { designFileName = currentFiles->getPhylipFile(); m->mothurOut("Using " + designFileName + " as phylip file."); m->mothurOutEndLine();
+ }else { m->mothurOut("You must provide an design file."); m->mothurOutEndLine(); abort = true; }
}
string temp = validParameter.validFile(parameters, "iters", false);