/**
* key is Element (Sequence/OTU/tree leaf), value is LCA, taxid, rank if ranks = null, then no
* rank column
*
* @param outFilePath
* @param elementTaxonMap
* @param ranks
* @throws java.io.IOException
*/
public static void writeElementTaxonomyMap(
Path outFilePath, SortedMap<String, Taxon> elementTaxonMap, Rank... ranks)
throws IOException {
BufferedWriter writer =
getWriter(outFilePath, "taxonomic mapping" + (ranks == null ? "" : " and assignment"));
int total = 0;
for (Map.Entry<String, Taxon> entry : elementTaxonMap.entrySet()) {
Taxon taxon = entry.getValue();
writer.write(entry.getKey() + "\t" + (taxon == null ? "" : taxon.getScientificName()));
writer.write(
"\t"
+ (taxon == null ? "" : taxon.getTaxId())
+ "\t"
+ (taxon == null ? "" : taxon.getRank()));
if (taxon != null && ranks != null) {
for (Rank rank : ranks) {
Taxon t = taxon.getParentTaxonOn(rank);
String str = ("no " + rank.toString()).toLowerCase();
writer.write("\t" + (t == null ? str : t.getScientificName()));
writer.write(
"\t" + (t == null ? str : t.getTaxId()) + "\t" + (t == null ? str : t.getRank()));
}
}
writer.write("\n");
total++;
}
writer.flush();
writer.close();
MyLogger.debug("Total entry in ElementTaxonomyMap = " + total);
}