/*
 * GenbankParser.java
 */
package org.ngbw.utils;


import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.util.regex.Pattern;


/**
 * 
 * @author Paul Hoover
 *
 */
class GenbankParser extends Parser {

	private static final Pattern m_fieldStartPattern = Pattern.compile("^\\S+.*$");
	private static final Pattern m_locusPattern = Pattern.compile("^LOCUS.*$");
	private static final Pattern m_definitionPattern = Pattern.compile("^DEFINITION.*$");
	private static final Pattern m_accessionPattern = Pattern.compile("^ACCESSION.*$");
	private static final Pattern m_versionPattern = Pattern.compile("^VERSION.*$");
	private static final Pattern m_sourcePattern = Pattern.compile("^SOURCE.*$");
	private static final Pattern m_recordEndPattern = Pattern.compile("^\\s*//\\s*$");
	private static final Pattern m_filterPattern = Pattern.compile("^\\s+/translation=.*$|^ORIGIN.*$");


	/**
	 * 
	 * @param input
	 */
	public GenbankParser(String input)
	{
		super(input, m_filterPattern);
	}

	/**
	 * 
	 * @param input
	 */
	public GenbankParser(byte[] input)
	{
		super(input, m_filterPattern);
	}

	/**
	 * 
	 * @param input
	 */
	public GenbankParser(InputStream input)
	{
		super(input, m_filterPattern);
	}

	/**
	 * 
	 * @param input
	 */
	public GenbankParser(Reader input)
	{
		super(input, m_filterPattern);
	}


	/**
	 * 
	 * @return
	 * @throws IOException
	 */
	public SequenceRecord nextRecord() throws IOException
	{
		if (!findFirstLine(m_locusPattern))
			return null;

		SequenceRecord record = new SequenceRecord();

		readAndStoreLine();

		while (true) {
			if (m_line == null)
				return null;

			if (m_definitionPattern.matcher(m_line).matches())
				parseDefinition(record);
			else if (m_accessionPattern.matcher(m_line).matches())
				parseAccession(record);
			else if (m_versionPattern.matcher(m_line).matches())
				parseVersion(record);
			else if (m_sourcePattern.matcher(m_line).matches())
				parseSource(record);
			else if (m_recordEndPattern.matcher(m_line).matches()) {
				record.completeSource = getCompleteSource();
				record.filteredSource = getFilteredSource();

				break;
			}
			else
				ignoreField();
		}

		return record;
	}

	/**
	 * 
	 * @param record
	 * @throws IOException
	 */
	private void parseDefinition(SequenceRecord record) throws IOException
	{
		StringBuilder field = new StringBuilder();
		String[] subStrings = m_line.split("\\s+", 2);

		if (subStrings.length > 1)
			field.append(subStrings[1]);

		while (true) {
			readAndStoreLine();

			if (m_line == null || m_fieldStartPattern.matcher(m_line).matches()) {
				record.name = field.toString();

				return;
			}

			field.append(' ');
			field.append(m_line.trim());
		}
	}

	/**
	 * 
	 * @param record
	 * @throws IOException
	 */
	private void parseAccession(SequenceRecord record) throws IOException
	{
		String[] subStrings = m_line.split("\\s+");

		if (subStrings.length > 1)
			record.primaryId = subStrings[1];

		readAndStoreLine();
	}

	/**
	 * 
	 * @param record
	 * @throws IOException
	 */
	private void parseVersion(SequenceRecord record) throws IOException
	{
		String[] subStrings = m_line.split("\\s+");

		if (subStrings.length == 3 && subStrings[2].startsWith("GI:")) {
			record.version = subStrings[1];
			record.alternativeId = subStrings[2].substring(3);
		}

		readAndStoreLine();
	}

	/**
	 * 
	 * @param record
	 * @throws IOException
	 */
	private void parseSource(SequenceRecord record) throws IOException
	{
		String[] subStrings = m_line.split("\\s+", 2);

		if (subStrings.length > 1)
			record.organism = subStrings[1];

		ignoreField();
	}

	/**
	 * 
	 * @throws IOException
	 */
	private void ignoreField() throws IOException
	{
		while (true) {
			readAndStoreLine();

			if (m_line == null || m_fieldStartPattern.matcher(m_line).matches())
				return;
		}
	}
}