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Variant annotation and effect prediction package.
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package org.snpeff.interval;

import java.util.HashMap;

/**
 * Convert chromosome names to simple names
 * @author pcingola
 */
public class ChromosomeSimpleName {

	public static final String CHROMO_PREFIX[] = { "chromosome", "chromo", "chr" }; //, "group", "scaffold", "contig", "supercontig", "supercont", "0" }; // Must be lower case (see method)
	private static ChromosomeSimpleName instance = new ChromosomeSimpleName();

	private final HashMap map;

	/**
	 * Get a simple name for the chromosome
	 */
	public static String get(String chrName) {
		return instance.simpleNameCache(chrName);
	}

	private ChromosomeSimpleName() {
		map = new HashMap();
	}

	/**
	 * Remove 'prefix' from 'chr'
	 */
	String removePrefix(String chr, String prefix) {
		String chrLower = chr.toLowerCase();
		String prefixLower = prefix.toLowerCase();

		// Remove prefix it it matches
		if (chrLower.startsWith(prefixLower)) return chr.substring(prefix.length());
		return chr;
	}

	/**
	 * Simplify chromosome name
	 */
	protected String simpleName(String chr) {
		if (chr == null) return "";
		chr = chr.trim();

		// Remove any prefix string until no change is made
		String chrPrev = "";
		do {
			chrPrev = chr;

			// If chr matches EXACTLY, we don't remove any prefix
			// E.g.:
			//		Let's assume that chr is 'Chromosome'
			//			i) If we remove prefix 'Chromosome', then we get an empty chromosome name, which is illegal.
			//			ii) If we remove "Chromo" (another prefix), the we get "some", which doesn't make any sense.
			//
			// So in case of ANY exact match, it's better not to remove any prefix.
			boolean exactMatch = false;
			for (String prefix : CHROMO_PREFIX)
				exactMatch |= chr.equalsIgnoreCase(prefix);

			// Remove all common prefixes
			if (!exactMatch) {
				for (String prefix : CHROMO_PREFIX) {
					chr = removePrefix(chr, prefix + ":");
					chr = removePrefix(chr, prefix + "_");
					chr = removePrefix(chr, prefix + "-");
					chr = removePrefix(chr, prefix);
				}
			}

			// Remove left zeros (unless the name is '0') and trim spaces
			if (!chr.equals("0")) chr = removePrefix(chr, "0");
			chr = chr.trim();

		} while (!chr.equals(chrPrev));

		return chr;
	}

	/**
	 * Query cache before simplifying name
	 */
	protected String simpleNameCache(String chrName) {
		String chr = map.get(chrName);
		if (chr == null) {
			chr = simpleName(chrName);
			map.put(chrName, chr);
		}
		return chr;
	}

}