public TaxonMappingOptions() {
super(TaxonMappingOptions.class);
beginAlignHorizontally(null, false);
mapFileOption = addFileSelectionOption("taxonMap", "Mapping File:", "");
addHelpButton(
"Help",
"This file should contain the mapping from your barcode sequence names as they appear in "
+ "your FASTA files to the genus and species of the barcode. You may choose your own separator and where "
+ "the taxons fall in each line.\n\n<strong>Note</strong>: The name must always be the first element.");
endAlignHorizontally();
useInputFiles =
addBooleanOption("useFasta", "Map using the sequence names in my input files", false);
useInputFiles.setDescription(
"This option causes the names of sequences contained in your FASTA file to be used "
+ "to obtain the mapping instead of a separate mapping file");
separatorOption =
addCustomOption(new NameSeparatorOption("separatorOption", "Separate each line with: "));
genusPartOption = addCustomOption(new NamePartOption("genusPartOption", "Genus is ", 1));
speciesPartOption = addCustomOption(new NamePartOption("speciesPartOption", "Species is ", 2));
useInputFiles.addDependent(mapFileOption, false);
}
public boolean getBoolean(String optionName) {
BooleanOption o;
synchronized (this) {
o = (BooleanOption) map.get(optionName);
}
return o.getValue();
}
public void set(String name, boolean value)
throws InvalidConfigValueException, NodeNeedRestartException {
BooleanOption o = (BooleanOption) map.get(name);
o.set(value);
}
