package ca.bcgsc.abyssexplorer.parsers;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import ca.bcgsc.abyssexplorer.graph.AbyssGraph;

/**
 * Custom parser for DOT output.
 * 
 * WARNING: VERSION NOT YET STABLE 
 * 
 * @author Cydney Nielsen
 * 
 */
public class DotParser implements GraphParser {
	
	BufferedReader inputStream;
	
	// first line of a graph
	protected static Pattern headerPattern = Pattern.compile("^digraph\\s*(\\S+)\\s*\\{\\s*$", Pattern.MULTILINE);
	// last line of a graph
	protected static Pattern footerPattern = Pattern.compile("^\\s*\\}\\s*$", Pattern.MULTILINE);
	protected static Pattern modePattern = Pattern.compile("^\\s*(\")?mode(\")?\\s*=\\s*(\")?(\\w+)(\")?;\\s*$", Pattern.MULTILINE);
	// vertex pattern - e.g. "0+"
	protected static Pattern vertexPattern = Pattern.compile("\"((\\d+)([+-]))\"", Pattern.MULTILINE);
	// adj pattern - e.g. "0+" -> { "513714-" "540790+" };
	protected static Pattern adjPattern = Pattern.compile("^\\s*\"(\\d+)([+-])\"(\\s*->\\s*\\{(( \"\\d+[+-]\")+) \\})?;\\s*$", Pattern.MULTILINE);
	// dist pattern - e.g. "0+"->"39+"[label=-25];
	protected static Pattern distPattern = Pattern.compile("^\\s*\"(\\d+[+-])\"\\s*->\\s*\"(\\d+[+-])\"\\s*\\[label\\s*=\\s*([+-]?\\d+)\\];\\s*$", Pattern.MULTILINE);

	protected Matcher hp;
	protected Matcher fp;
	protected Matcher mp;
	protected Matcher vp; 
	protected Matcher ap;
	protected Matcher dp;
	
	protected Object dummyO = new Object(); 
	
	protected void regexSetup(CharSequence s) {
		hp = headerPattern.matcher(s);
		fp = footerPattern.matcher(s);
		mp = modePattern.matcher(s);
		vp = vertexPattern.matcher(s);
		ap = adjPattern.matcher(s);
		dp = distPattern.matcher(s);
	}
	
	public void open(File f) throws IOException {
		String fName = f.getAbsolutePath();
		try {
			inputStream = new BufferedReader(new FileReader(fName));
		} catch (FileNotFoundException e) {
			throw (new IOException("No such file: " + fName));
		}
	}
	
	public void close() throws IOException {
		inputStream.close();
	}
	
	public AbyssGraph initializeGraph() throws IOException {
		boolean foundAdjGraph = false;
		// count the number of vertices
		int vCount = 0; 
		// find the largest contig label id 
		// not equivalent to single-end contig count in ABySS
		int maxE = 0;
		while (inputStream.ready()) {
			Object o = parseNextLine();
			if (o == null) {continue;} // no match to known patterns
			if (o instanceof AdjacentContigs) {
				foundAdjGraph = true;
				vCount += 1;
				// one connection from single source vertex to each target
				String label = ((AdjacentContigs) o).getLabel();
				int e = Integer.parseInt(label.replace("+", "").replace("-", ""));
				if (e > maxE) { maxE = e; }
				// System.out.println(vCount + " " + maxE);
			}
		}
		int eCount = maxE + 1; // 0 based labels
		
		if (!foundAdjGraph) { 
			throw (new IOException("DOT file must contain an 'adj' graph"));
		}
		
		System.out.println("found " + vCount + " vertices and " + eCount + " edges");
		
		// actual vCount typically < eCount, but > eCount/2, so using vCount=eCount reasonable estimate
		AbyssGraph g = new AbyssGraph(eCount, eCount);
		return g;
	}
	
	/**
	 * Returns null at end of file
	 */
	public Object parseNextLine() throws IOException {
		String s = inputStream.readLine();
		if (s == null) { return null; }
		regexSetup(s);
		// first try to match adjaceny line
		Object o = matchAdj(s);
		if (o == null) {
			// then try to match dist line
			o = matchDist(s);
			if (o == null) {
				o = dummyO;
			}
		}
		return o;
	}
	
	public AdjacentContigs matchAdj(String s) {
		if (!ap.find()) { return null; }
		AdjacentContigs aContigs;
		int mStart = ap.start();
		// find source vertex pattern
		vp.find(mStart);
		aContigs = new AdjacentContigs(vp.group(1));
		mStart = vp.end();
		// find all partner vertex patterns
		while (vp.find(mStart)) {
			aContigs.addOutbound(vp.group(1));
			mStart = vp.end();
		}
		return aContigs;
	}
	
	public PairedEndPartners matchDist(String s) {
		if (!dp.find()) { return null; }
		String src = dp.group(1); int sId; byte sStrand; 
		if (src.endsWith("+")) {
			sId = Integer.parseInt(src.replace("+",""));
			sStrand = 0;
		} else {
			sId = Integer.parseInt(src.replace("-", ""));
			sStrand = 1;
		}
		String des = dp.group(2); int dId; byte dStrand;
		if (des.endsWith("+")) {
			dId = Integer.parseInt(des.replace("+", ""));
			dStrand = 0;
		} else {
			dId = Integer.parseInt(des.replace("-", ""));
			dStrand = 1;
		}
		int dist = Integer.parseInt(dp.group(3));
		PairedEndPartners d = new PairedEndPartners(sId, sStrand, dId, dStrand, dist);
		return d;
	}
	
}