{
case "HMM Name":
name = arg.getValue();
+ name = name.trim();
break;
case "Use Reference Annotation":
command += "--hand ";
}
}
- name = name.trim();
+
if (name == null || "".equals(name))
{
}
}
- command += "-n " + name + cmds.SPACE;
+ command += "-n " + name.replace(' ', '_') + cmds.SPACE;
if (!alignment.isNucleotide())
{
command += cmds.FORCEAMINO; // TODO check for rna