/**
* 1st column is Element (Sequence/OTU/tree leaf), 2nd is taxid
*
* @param inFilePath
* @return
* @throws IOException
*/
public static SortedMap<String, Taxon> importElementTaxonomyMap(Path inFilePath)
throws IOException, XMLStreamException {
SortedMap<String, Taxon> otuTaxaMap = new TreeMap<>();
BufferedReader reader = getReader(inFilePath, "Element taxonomy mapping");
Separator lineSeparator = new Separator("\t");
String line = reader.readLine();
while (line != null) {
if (hasContent(line)) { // not comments or empty
String[] items = lineSeparator.parse(line);
if (items.length < 2)
throw new IllegalArgumentException(
"Invalid file format for Element taxonomy mapping, line : " + line);
if (otuTaxaMap.containsKey(items[0]))
throw new IllegalArgumentException("Find duplicate name for " + items[0]);
Taxon taxon = TaxonomyPool.getAndAddTaxIdByMemory(items[1]);
otuTaxaMap.put(items[0], taxon);
}
line = reader.readLine();
}
reader.close();
if (otuTaxaMap.size() < 1) throw new IllegalArgumentException("OTU taxonomy map is empty !");
return otuTaxaMap;
}
public static TaxonSet importTaxa(Path taxaTSV) throws IOException {
TaxonSet taxonSet = new TaxonSet();
BufferedReader reader = getReader(taxaTSV, "taxa");
Separator lineSeparator = new Separator("\t");
String line = reader.readLine();
while (line != null) {
if (hasContent(line)) { // not comments or empty
String[] items = lineSeparator.parse(line);
// if (items.length < 2)
// throw new IllegalArgumentException("Invalid file format for taxa
// traits mapping, line : " + line);
taxonSet.addUniqueElement(items[0]);
}
line = reader.readLine();
}
reader.close();
if (taxonSet.size() < 1) throw new IllegalArgumentException("It needs at least one taxon !");
return taxonSet;
}