/*
 File: AnnotationFlatFileReader.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.
 */

// AnnotationFlatFileReader.java
package cytoscape.data.annotation.readers;

import cytoscape.data.annotation.Annotation;

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.io.File;

import java.util.Vector;


/**
 *
 */
public class AnnotationFlatFileReader {
	Annotation annotation;
	String annotationType;
	String species;
	String curator;
	String filename;
	File directoryAbsolute;
	String fullText;
	String[] lines;
	Vector extractedLines;
	boolean flip;
	Thesaurus thr;

	/**
	 * Creates a new AnnotationFlatFileReader object.
	 *
	 * @param file  DOCUMENT ME!
	 *
	 * @throws Exception  DOCUMENT ME!
	 */
	public AnnotationFlatFileReader(File file) throws Exception {
		this(file.getPath(), null);
	}

	/*
	 * New const. written by Kei Ono (kono@uscd.edu) This accept new readers
	 * written by Nerius.
	 */

	/**
	 * Creates a new AnnotationFlatFileReader object.
	 *
	 * @param rd  DOCUMENT ME!
	 * @param th  DOCUMENT ME!
	 * @param isFlip  DOCUMENT ME!
	 *
	 * @throws Exception  DOCUMENT ME!
	 */
	public AnnotationFlatFileReader(final BufferedReader rd, Thesaurus th, boolean isFlip)
	    throws Exception {
		fullText = null;
		extractedLines = new Vector();
		this.thr = th;
		this.flip = isFlip;

		String curLine = null;

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

		parseHeader(lines[0]);
		parse();
	}

	/**
	 * Creates a new AnnotationFlatFileReader object.
	 *
	 * @param filename  DOCUMENT ME!
	 * @param th  DOCUMENT ME!
	 *
	 * @throws Exception  DOCUMENT ME!
	 */
	public AnnotationFlatFileReader(String filename, Thesaurus th) throws Exception {
		// CyLogger.getLogger().info ("AnnotationFlatFileReader on " + filename);
		this.filename = filename;
		this.thr = th;

		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;
		}

		/***********************************************************************
		 * this.species = species; this.annotationType = annotationType;
		 * directoryAbsolute = file.getAbsoluteFile().getParentFile ();
		 * TextFileReader reader = new TextFileReader (file.getPath ());
		 * reader.read (); fullText = reader.getText ();
		 **********************************************************************/
		lines = fullText.split("\n");
		// CyLogger.getLogger().info ("number of lines: " + lines.length);
		parseHeader(lines[0]);
		parse();
	}

	private int stringToInt(String s) {
		try {
			return Integer.parseInt(s);
		} catch (NumberFormatException nfe) {
			return -1;
		}
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param firstLine DOCUMENT ME!
	 *
	 * @throws Exception DOCUMENT ME!
	 * @throws IllegalArgumentException DOCUMENT ME!
	 */
	public void parseHeader(String firstLine) throws Exception {
		String[] tokens = firstLine.trim().split("\\)");

		String errorMsg = "error in AnnotationFlatFileReader.parseHeader ().\n";
		errorMsg += ("First line of " + filename + " must have form:\n");
		errorMsg += "   (species=Homo sapiens) (type=Biological Process) (curator=GO)\n";
		errorMsg += "instead found:\n";
		errorMsg += ("   " + firstLine + "\n");

		if (tokens.length != 3)
			throw new IllegalArgumentException(errorMsg);

		for (int i = 0; i < tokens.length; i++) {
			String[] subTokens = tokens[i].split("=");

			if (subTokens.length != 2)
				throw new IllegalArgumentException(errorMsg);

			String name = subTokens[0].trim();
			String value = subTokens[1].trim();

			if (name.equalsIgnoreCase("(species"))
				species = value;
			else if (name.equalsIgnoreCase("(type"))
				annotationType = value;
			else if (name.equalsIgnoreCase("(curator"))
				curator = value;
		}
	} // parseHeader

	private void parse() throws Exception {
		annotation = new Annotation(species, annotationType, curator);

		String key = null;

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

			if (line.length() < 2)
				continue;

			String[] tokens = line.split("=");
			String entityName = tokens[0].trim();
			int id = stringToInt(tokens[1].trim());

			// Swap first alias and label
			if (flip == false) {
				annotation.add(entityName, id);

				String[] syno = thr.getAllCommonNames(entityName);

				for (int idx = 0; idx < syno.length; idx++) {
					annotation.add(syno[idx], id);
				}
			} else if (flip == true) {
				// CyLogger.getLogger().info ( "EntityName is " + entityName );
				key = thr.getNodeLabel(entityName);

				if (key != null) {
					// CyLogger.getLogger().info ("Found: Key is " + key );
					annotation.add(key, id);
				} else {
					// annotation.add ( "Undef", id);
				}
			}

			// CyLogger.getLogger().info ("Anno# Key = " + entityName + ", ID = " +
			// id);
		}
	} // parse

	/**
	 *  DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public Annotation getAnnotation() {
		return annotation;
	}
} // class AnnotationFlatFileReader