org.biopax.paxtools.pattern.util.HGNC Maven / Gradle / Ivy

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package org.biopax.paxtools.pattern.util;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;

/**
 * This class provides a mapping between HGNC IDs and Symbols.
 * We periodically, manually download
 * 
 * the ID mapping file from genenames.org
 *
 * @author Ozgun Babur
 */
public class HGNC
{
	private static Map sym2id;
	private static Map id2sym;
	private static Map old2new;

	public static String getSymbol(String idOrSymbol)
	{
		if (id2sym.containsKey(idOrSymbol)) return id2sym.get(idOrSymbol);
		else if (sym2id.containsKey(idOrSymbol)) return idOrSymbol;
		else if (old2new.containsKey(idOrSymbol)) return old2new.get(idOrSymbol);
		else if (!idOrSymbol.toUpperCase().equals(idOrSymbol))
			return getSymbol(idOrSymbol.toUpperCase());
		else return null;
	}

	static
	{
		try
		{
			sym2id = new HashMap();
			id2sym = new HashMap();
			old2new = new HashMap();
			BufferedReader reader = new BufferedReader(new InputStreamReader(
				HGNC.class.getResourceAsStream("hgnc.txt")));

			reader.readLine(); //skip header
			for (String line = reader.readLine(); line != null; line = reader.readLine())
			{
				String[] token = line.split("\t");
				String sym = token[1].trim();
				String id = token[0].trim();
				sym2id.put(sym, id);
				id2sym.put(id, sym);

				if (token.length > 2)
				{
					String olds = token[2];
					for (String old : olds.split(","))
					{
						old = old.trim();
						old2new.put(old, sym);
					}
				}
			}
			reader.close();
		}
		catch (FileNotFoundException e)
		{
			e.printStackTrace();
		}
		catch (IOException e)
		{
			e.printStackTrace();
		}
	}
}