/*--------------------------------------------------------------------------
    *  Copyright 2009 utgenome.org
    *
    *  Licensed under the Apache License, Version 2.0 (the "License");
    *  you may not use this file except in compliance with the License.
    *  You may obtain a copy of the License at
    *
    *     http://www.apache.org/licenses/LICENSE-2.0
    *
   *  Unless required by applicable law or agreed to in writing, software
   *  distributed under the License is distributed on an "AS IS" BASIS,
   *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   *  See the License for the specific language governing permissions and
   *  limitations under the License.
   *--------------------------------------------------------------------------*/
  //--------------------------------------
  // utgb-core Project
  //
  // WIG2Silk.java
  // Since: 2009/05/07
  //
  //--------------------------------------
  package org.utgenome.format.wig;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.FileReader;
  import java.io.IOException;
  import java.io.PrintWriter;
  import java.io.Reader;
  import java.io.StringReader;
  import java.io.StringWriter;
  import java.util.ArrayList;
  
  import org.antlr.runtime.ANTLRReaderStream;
  import org.antlr.runtime.CommonTokenStream;
  import org.antlr.runtime.RecognitionException;
  import org.antlr.runtime.tree.Tree;
  import org.utgenome.UTGBException;
  import org.xerial.core.XerialException;
  import org.xerial.lens.Lens;
  import org.xerial.util.log.Logger;
  
  /**
   * @author yoshimura
   * 
   */
  public class WIG2Silk {
  
  	private static Logger _logger = Logger.getLogger(WIG2Silk.class);
  
  	private final BufferedReader reader;
  
  	public static class WIGHeaderDescription {
  		String name;
  		ArrayList<WIGHeaderAttribute> attributes = new ArrayList<WIGHeaderAttribute>();
  
  		public void setName(String name) {
  			this.name = name;
  		}
  
  		public void addAttribute(WIGHeaderAttribute attribute) {
  			attributes.add(attribute);
  		}
  
  		@Override
  		public String toString() {
  			return String.format("name=%s, attributes=%s", name, attributes.toString());
  		}
  	}
  
  	public static class WIGHeaderAttribute {
  		String name;
  		String value;
  
  		public void setName(String name) {
  			this.name = name;
  		}
  
  		public void setValue(String value) {
  			this.value = value;
  		}
  
  		@Override
  		public String toString() {
  			return String.format("{name=%s, value=%s}", name, value);
  		}
  	}
  
  	public WIG2Silk(File wigFile) throws IOException {
  		this(new FileReader(wigFile));
  	}
  
  	/**
  	 * 
  	 * @param wigFile
  	 * @throws IOException
  	 */
  	public WIG2Silk(Reader wigFile) throws IOException {
 
 		// track = new WIGHeaderDescription();
 		// genes = new ArrayList<String[]>();
 
 		this.reader = new BufferedReader(wigFile);
 
 	}
 
 	/**
 	 * 
 	 * @param out
 	 * @throws IOException
 	 * @throws UTGBShellException
 	 */
 
 	public void toSilk(PrintWriter out) throws IOException, UTGBException {
 
 		// print header line
 		out.print("%silk(version:1.0)");
 		out.flush();
 
 		int lineNum = 1;
 		for (String line; (line = reader.readLine()) != null; lineNum++) {
 
 			try {
 				if (line.startsWith("#") || line.length() == 0) {
 				}
 				else if (line.startsWith("browser")) {
 					// this.browser = readTrackLine(line,i);
 				}
 				else if (line.startsWith("track")) {
 					// print track line
 					StringBuffer sb = new StringBuffer("\n-track(");
 					sb = readHeaderLine(sb, line);
 					out.println(sb.toString());
 					out.flush();
 				}
 				else if (line.startsWith("variableStep")) {
 					StringBuffer sb = new StringBuffer(" -coordinate(stepType:variable, ");
 					sb = readHeaderLine(sb, line);
 					sb.append("\n  -data(start, value)|");
 					out.println(sb.toString());
 					out.flush();
 				}
 				else if (line.startsWith("fixedStep")) {
 					StringBuffer sb = new StringBuffer(" -coordinate(stepType:fixed, ");
 					sb = readHeaderLine(sb, line);
 					sb.append("\n  -data(value)|");
 					out.println(sb.toString());
 					out.flush();
 				}
 				else {
 					String[] lineValues = readWIGLine(line, lineNum);
 					StringBuilder sb = new StringBuilder();
 					for (String value : lineValues) {
 						sb.append(value + "\t");
 					}
 					out.println(sb.toString().trim());
 					out.flush();
 				}
 			}
 			catch (RecognitionException e) {
 				throw new UTGBException(String.format("line %d: %s", lineNum, e));
 			}
 			catch (XerialException e) {
 				throw new UTGBException(String.format("line %d: %s", lineNum, e));
 			}
 		}
 	}
 
 	public String toSilk() throws IOException, UTGBException {
 		StringWriter out = new StringWriter();
 		toSilk(new PrintWriter(out));
 		return out.toString();
 	}
 
 	private static String[] readWIGLine(String line, int lineNo) {
 		String[] temp = line.replace(" ", "\t").trim().split("\t+");
 		// split by tab or space
 		if (temp.length > 2) {
 			_logger.error("Error data -> line:" + lineNo);
 		}
 		return temp;
 	}
 
 	private static StringBuffer readHeaderLine(StringBuffer sb, String line) throws IOException, XerialException, RecognitionException {
 		WIGLexer lexer = new WIGLexer(new ANTLRReaderStream(new StringReader(line)));
 		CommonTokenStream tokens = new CommonTokenStream(lexer);
 
 		WIGParser parser = new WIGParser(tokens);
 		WIGParser.description_return ret = parser.description();
 
 		for (WIGHeaderAttribute a : Lens.loadANTLRParseTree(WIGHeaderDescription.class, (Tree) ret.getTree(), WIGParser.tokenNames).attributes) {
 			sb.append(a.name + ":");
 			if ((a.value.contains(",") || a.value.contains(" ") || a.value.contains(":")) && !a.value.startsWith("\"") && !a.value.endsWith("\"")) {
 				sb.append("\"" + a.value + "\", ");
 			}
 			else {
 				sb.append(a.value + ", ");
 			}
 		}
 		return sb.delete(sb.lastIndexOf(","), sb.length()).append(")");
 	}
 
 	private static String changeRGB2Hex(String rgb) {
 		String[] temp = rgb.split(",");
 		StringBuffer ret = new StringBuffer("\"#");
 		if (temp.length >= 3) {
 			for (int i = 0; i < 3; i++) {
 				if (Integer.valueOf(temp[i]) > 255 || Integer.valueOf(temp[i]) < 0) {
 					System.err.println("Warn : out of color range 0-255");
 					return "";
 				}
 				if (Integer.toHexString(Integer.valueOf(temp[i])).length() == 1) {
 					ret.append("0");
 				}
 				ret.append(Integer.toHexString(Integer.valueOf(temp[i])));
 			}
 			return ret.append("\"").toString();
 		}
 		else {
 			return "";
 		}
 	}
 }