/*
 File: ThesaurusFlatFileReader.java

 Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)

 The Cytoscape Consortium is:
 - Institute for Systems Biology
 - University of California San Diego
 - Memorial Sloan-Kettering Cancer Center
 - Institut Pasteur
 - Agilent Technologies

 This library is free software; you can redistribute it and/or modify it
 under the terms of the GNU Lesser General Public License as published
 by the Free Software Foundation; either version 2.1 of the License, or
 any later version.

 This library is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
 MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
 documentation provided hereunder is on an "as is" basis, and the
 Institute for Systems Biology and the Whitehead Institute
 have no obligations to provide maintenance, support,
 updates, enhancements or modifications.  In no event shall the
 Institute for Systems Biology and the Whitehead Institute
 be liable to any party for direct, indirect, special,
 incidental or consequential damages, including lost profits, arising
 out of the use of this software and its documentation, even if the
 Institute for Systems Biology and the Whitehead Institute
 have been advised of the possibility of such damage.  See
 the GNU Lesser General Public License for more details.

 You should have received a copy of the GNU Lesser General Public License
 along with this library; if not, write to the Free Software Foundation,
 Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
 */

// ThesaurusFlatFileReader.java

// ------------------------------------------------------------------------------
// $Revision: 17791 $
// $Date: 2009-08-12 11:52:17 -0500 (Wed, 12 Aug 2009) $
// $Author: noelr $
// ------------------------------------------------------------------------------
package cytoscape.data.synonyms.readers;

import cytoscape.data.readers.TextFileReader;
import cytoscape.data.readers.TextHttpReader;
import cytoscape.data.readers.TextJarReader;

import cytoscape.data.synonyms.Thesaurus;
import cytoscape.logger.CyLogger;

// ------------------------------------------------------------------------------
import java.io.BufferedReader;

import java.util.Vector;


/**
 * Read synonyms from flat file.
 *
 * @author kono
 *
 */
public class ThesaurusFlatFileReader {
	Thesaurus thesaurus;
	String fullText;
	String[] lines;
	boolean flip;

	// -------------------------------------------------------------------------
	/**
	 * Creates a new ThesaurusFlatFileReader object.
	 *
	 * @param filename  DOCUMENT ME!
	 *
	 * @throws Exception  DOCUMENT ME!
	 */
	public ThesaurusFlatFileReader(String filename) throws Exception {
		flip = false;

		try {
			if (filename.trim().startsWith("jar://")) {
				TextJarReader reader = new TextJarReader(filename);
				reader.read();
				fullText = reader.getText();
			} else if (filename.trim().startsWith("http://")) {
				TextHttpReader reader = new TextHttpReader(filename);
				reader.read();
				fullText = reader.getText();
			} else {
				TextFileReader reader = new TextFileReader(filename);
				reader.read();
				fullText = reader.getText();
			}
		} catch (Exception e0) {
			CyLogger.getLogger().warn("-- Exception while reading ontology flat file " + filename, e0);

			return;
		}

		read();
	}

	/**
	 * Creates a new ThesaurusFlatFileReader object.
	 *
	 * @param rd  DOCUMENT ME!
	 * @param isFlip  DOCUMENT ME!
	 *
	 * @throws Exception  DOCUMENT ME!
	 */
	public ThesaurusFlatFileReader(final BufferedReader rd, boolean isFlip)
	    throws Exception {
		Vector extractedLines = null;

		// Flip or not
		flip = isFlip;

		fullText = null;
		extractedLines = new Vector();

		String curLine = null;

        try {
            while (null != (curLine = rd.readLine())) {
                extractedLines.add(curLine);

    			// CyLogger.getLogger().info( curLine );
        	}
        }
        finally {
            if (rd != null) {
                rd.close();
            }
        }

		Object[] entireFile = extractedLines.toArray();
		lines = new String[entireFile.length];

		try {
			System.arraycopy(entireFile, 0, lines, 0, lines.length);
		} catch (Exception e) {
			throw e;
		}

		read();
	}

	// -------------------------------------------------------------------------
	private void read() throws Exception {
		if (fullText != null) {
			lines = fullText.split("\n");
		}

		String species = lines[0].trim();
		thesaurus = new Thesaurus(species);

		for (int i = 1; i < lines.length; i++) {
			String line = lines[i].trim();

			// If comment line or too short, just skip
			if (line.startsWith("#"))
				continue;

			if (line.length() < 3)
				continue;

			String[] tokens = lines[i].split("\\s+", 0);

			if (tokens.length < 2)
				continue;

			// Node label.
			String canonicalName = tokens[0].trim();

			// This is the first element in the Aliases
			String commonName = tokens[1].trim();

			if (canonicalName.length() == 0)
				continue;

			if (commonName.length() == 0)
				continue;

			// Flipping canonical and aliases.
			if (flip == false) {
				thesaurus.add(canonicalName, commonName);

				// CyLogger.getLogger().info("Cannonical = " + canonicalName
				// + " Common 1 = " + commonName);
				for (int t = 2; t < tokens.length; t++) {
					thesaurus.addAlternateCommonName(canonicalName, tokens[t].trim());

					// CyLogger.getLogger().info(" Cannonical = " + canonicalName + "
					// Common " + t + " = " + tokens [t].trim() );
				} // for i
			} else if (flip == true) {
				// If flip is true, swap the fields.
				thesaurus.add(commonName, canonicalName);

				// Then, add Aliases
				for (int t = 2; t < tokens.length; t++) {
					thesaurus.addAlternateCommonName(commonName, tokens[t].trim());
				}
			}
		}
	} // read

	// -------------------------------------------------------------------------
	/**
	 *  DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public Thesaurus getThesaurus() {
		return thesaurus;
	}

	// -------------------------------------------------------------------------
} // class ThesaurusFlatFileReader