ConsensusMetaMaker.java

package org.seqcode.viz.metaprofile;

import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.Vector;

import org.seqcode.data.io.BackgroundModelIO;
import org.seqcode.data.motifdb.MarkovBackgroundModel;
import org.seqcode.data.motifdb.WeightMatrix;
import org.seqcode.genome.Genome;
import org.seqcode.genome.Species;
import org.seqcode.genome.location.Point;
import org.seqcode.gseutils.Args;
import org.seqcode.gseutils.NotFoundException;
import org.seqcode.gseutils.Pair;
import org.seqcode.motifs.ConsensusSequence;
import org.seqcode.viz.metaprofile.swing.MetaFrame;
import org.seqcode.viz.metaprofile.swing.MetaNonFrame;


public class ConsensusMetaMaker {
	private static boolean batchRun = false;
	private static boolean cluster = false;
	private static boolean usingColorQuanta=false;
	private static double[] colorQuanta=null;
	
	public static void main(String[] args) throws IOException, ParseException {
		try {
			if(args.length < 2){ printError();}
			
			Pair<Species, Genome> pair = Args.parseGenome(args);
			Genome gen = pair.cdr();
			int winLen = Args.parseInteger(args,"win", 10000);
			int bins = Args.parseInteger(args,"bins", 100);
			String profilerType = Args.parseString(args, "profiler", "consensus");	
			String cons = Args.parseString(args,"consensus", null);
			ConsensusSequence consensus = new ConsensusSequence(cons);
			double mismatchthres = Args.parseDouble(args, "mismatch", 0);
			char watsoncrick =  Args.parseString(args,"watsoncrick", ".").charAt(0);
			String peakFile = Args.parseString(args, "peaks", null);
			String outName = Args.parseString(args, "out", "meta");
			boolean useCache = Args.parseFlags(args).contains("cache") ? true : false;
			String seqPathName="";
			if(useCache){
				seqPathName = Args.parseString(args, "seq", "");
			}
			if(Args.parseFlags(args).contains("batch")){batchRun=true;}
			if(Args.parseFlags(args).contains("cluster")){cluster=true;}
			if(Args.parseArgs(args).contains("quanta")){
				usingColorQuanta=true; 
				for(int a=0; a<args.length; a++){
					if(args[a].equals("--quanta")){
						int numQ=new Integer(args[a+1]);
						colorQuanta=new double[numQ];
						for(int q=0; q<numQ && (a+2+q)<args.length; q++){
							colorQuanta[q]=new Double(args[a+2+q]);
						}
					}
				}
				mismatchthres = colorQuanta[0];
			}
			Color c = Color.blue;
			String newCol = Args.parseString(args, "color", "blue");
			if(newCol.equals("red"))
				c=Color.red;
			if(newCol.equals("green"))
				c=new Color(0,153,0);
			if(newCol.equals("black"))
				c=Color.black;
		
			
			if(gen==null || consensus==null){printError();}
	
			BinningParameters params = new BinningParameters(winLen, bins);
			System.out.println("Binding Parameters:\tWindow size: "+params.getWindowSize()+"\tBins: "+params.getNumBins());
		
			
			PointProfiler profiler=null;
			boolean normalizeProfile=false;
			if(profilerType.equals("consensus")){
				System.out.println("Loading data...");
				profiler = new ConsensusProfiler(params, gen, consensus, mismatchthres, useCache, seqPathName, watsoncrick);
			}
			 
			if(batchRun){
				System.setProperty("java.awt.headless", "true");
				System.out.println("Batch running...");
				MetaNonFrame nonframe = new MetaNonFrame(gen, params, profiler, normalizeProfile, false);
				if(usingColorQuanta)
					nonframe.setLinePanelColorQuanta(colorQuanta);
				nonframe.setColor(c);
				MetaProfileHandler handler = nonframe.getHandler();
				if(peakFile != null){
					Vector<Point> points = nonframe.getUtils().loadPoints(new File(peakFile));
					handler.addPoints(points);
				}else{
					Iterator<Point> points = nonframe.getUtils().loadTSSs("refGene");
					handler.addPoints(points);
				}
				while(handler.addingPoints()){}
				if(cluster)
					nonframe.clusterLinePanel();
				//Set the panel sizes here...
				nonframe.setLineMin(0);
				nonframe.saveImages(outName);
				nonframe.savePointsToFile(outName);
				System.out.println("Finished");
			}else{
				System.out.println("Initializing Meta-point frame...");
				MetaFrame frame = new MetaFrame(gen, params, profiler, normalizeProfile);
				if(usingColorQuanta)
					frame.setLinePanelColorQuanta(colorQuanta);
				frame.setColor(c);
				frame.startup();
				MetaProfileHandler handler = frame.getHandler();
				if(peakFile != null){
					Vector<Point> points = frame.getUtils().loadPoints(new File(peakFile));
					handler.addPoints(points);
				}
			}
		} catch (NotFoundException e) {
			e.printStackTrace();
		} catch (IOException e) {
			e.printStackTrace();
		}
	}
	
	private static void printError(){
		System.err.println("Usage: ConsensusMetaMaker --species <organism;genome> \n" +
				"--win <profile width> --bins <num bins> \n" +
				"--profiler <consensus> \n" +
				"--consensus <IUPAC consensus> \n" +
				"--mismatch <mismatch threshold> \n" +
				"--peaks <peaks file name> --out <output root name> \n" +
				"--color <red/green/blue> \n" +
				"--cluster [flag to cluster in batch mode] \n" +
				"--cache <flag to use cache while loading sequences> AND --seq <Full path of the sequence> \n" +
				"--watsoncrick <W/C/.>"+
				"--batch [a flag to run without displaying the window]");
		System.exit(1);
	}

}