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Variant annotation and effect prediction package.

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package org.snpeff.sam;

import org.snpeff.util.Gpr;

/**
 * SQ header: Reference sequence dictionary. The order of @SQ lines defines the alignment sorting order.
 * 
 * @author pcingola
 */
public class SamHeaderRecordSq extends SamHeaderRecord {

	String sequenceName, assembly, md5, species, uri;
	int length;

	public SamHeaderRecordSq(String line) {
		super(line, "SQ");
	}

	public String getAssembly() {
		return assembly;
	}

	public int getLength() {
		return length;
	}

	public String getMd5() {
		return md5;
	}

	public String getSequenceName() {
		return sequenceName;
	}

	public String getSpecies() {
		return species;
	}

	public String getUri() {
		return uri;
	}

	@Override
	protected void init() {
		sequenceName = assembly = md5 = species = uri = "";
		length = 0;
	}

	@Override
	protected void parseField(String tag, String value) {
		if( tag.equals("SN") ) sequenceName = value;
		else if( tag.equals("LN") ) length = Gpr.parseIntSafe(value);
		else if( tag.equals("AS") ) assembly = value;
		else if( tag.equals("M5") ) md5 = value;
		else if( tag.equals("SP") ) species = value;
		else if( tag.equals("UR") ) uri = value;
		else Gpr.debug("Unknown tag '" + tag + "' for header record type '" + recordTypeCode + "'.");
	}

	@Override
	public String toString() {
		StringBuilder sb = new StringBuilder();
		sb.append('@' + recordTypeCode);

		if( !sequenceName.isEmpty() ) sb.append("\tSN:" + sequenceName);
		if( length > 0 ) sb.append("\tLN:" + length);
		if( !assembly.isEmpty() ) sb.append("\tAS:" + sequenceName);
		if( !md5.isEmpty() ) sb.append("\tM5:" + sequenceName);
		if( !species.isEmpty() ) sb.append("\tSP:" + sequenceName);
		if( !uri.isEmpty() ) sb.append("\tUR:" + sequenceName);

		return sb.toString();
	}

}