AlignmentSample.java

package statalign.postprocess.plugins.benchmarks;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;

public class AlignmentSample implements Serializable {
	
	/**
	 * 
	 */
	private static final long serialVersionUID = 8798582281020900675L;
	public Alignment reference = new Alignment();
	public Alignment mpd = new Alignment();
	public ArrayList<Double> posteriors = new ArrayList<Double>();
	public ArrayList<Alignment> samples = new ArrayList<Alignment>();

	public String toString() {
		String ret = "";
		ret += "%reference\n" + reference.toString();
		for (int i = 0; i < samples.size(); i++) {
			ret += "%" + i + "\n";
			ret += samples.get(i);
		}
		ret += "%mpd\n" + mpd.toString();
		ret += "%posteriors\n";
		for (int i = 0; i < posteriors.size(); i++) {
			ret += posteriors.get(i) + "\n";
		}
		return ret;
	}
	

	/**
	 * Loads an alignment sample object from a file.
	 * @param file
	 * @return
	 */
	public static AlignmentSample loadAlignments(File file) {

		AlignmentSample sample = new AlignmentSample();
		try {
			BufferedReader buffer = new BufferedReader(new FileReader(file));
			String textline = null;

			String alignmentString = "";
			String name = null;

			ArrayList<String> sequences = new ArrayList<String>();
			ArrayList<String> sequenceNames = new ArrayList<String>();
			while ((textline = buffer.readLine()) != null) {
				//System.out.println(textline);
				if (textline.startsWith("%")) {
					if(name == null)
					{
						
					}
					else
					if (name.equalsIgnoreCase("%reference")) {
						sample.reference.sequences = sequences;
						sample.reference.sequenceNames = sequenceNames;
					} else if (name.equalsIgnoreCase("%mpd")) {
						sample.mpd.sequences = sequences;
						sample.mpd.sequenceNames = sequenceNames;
					}
					else
						if(name.equalsIgnoreCase("%posteriors"))
						{
							
						}
						else {
							Alignment alignment = new Alignment();
							alignment.sequences = sequences;
							alignment.sequenceNames = sequenceNames;
							sample.samples.add(alignment);
						}

					
						name = textline;
						if("%posteriors".equals(name))
						{
							for(int i = 0 ; (textline = buffer.readLine()) != null && !textline.startsWith("%") ; i++)
							{
								sample.posteriors.add(new Double(textline));
							}
							
							if(textline != null && textline.startsWith("%"))
							{
								name = textline;
								System.out.println("#"+name);

								//''sequences = new ArrayList<String>();
								//'sequenceNames = new ArrayList<String>();
							}
						}

						if(!alignmentString.equals(""))
						{
							parseAlignmentString(alignmentString, sequences, sequenceNames);
							alignmentString = "";
	
							sequences = new ArrayList<String>();
							sequenceNames = new ArrayList<String>();
						}
				} else {
					alignmentString += textline + "\n";
				}
			}
			

			if(name == null)
			{
				
			}
			else
			if (name.equalsIgnoreCase("%reference")) {
				sample.reference.sequences = sequences;
				sample.reference.sequenceNames = sequenceNames;
			} else if (name.equalsIgnoreCase("%mpd")) {
				sample.mpd.sequences = sequences;
				sample.mpd.sequenceNames = sequenceNames;
			}
			else
			if(name.equalsIgnoreCase("%posteriors"))
			{
				
			}
			else {
				Alignment alignment = new Alignment();
				alignment.sequences = sequences;
				alignment.sequenceNames = sequenceNames;
				sample.samples.add(alignment);
			}

			if(!alignmentString.equals(""))
			{
				parseAlignmentString(alignmentString, sequences, sequenceNames);
				alignmentString = "";
				
			}
			buffer.close();
		} catch (IOException ex) {
			ex.printStackTrace();
		}

		return sample;
	}
	
	/**
	 * Fills a vector of sequences and vector of sequence names from a specified fasta alignment string.
	 * @param alignmentString
	 * @param sequences
	 * @param sequenceNames
	 */
	public static void parseAlignmentString(String alignmentString, ArrayList<String> sequences,  ArrayList<String> sequenceNames)
	{

		String seq = "";
		String name = "";
		String [] split = alignmentString.split("\n");
		for(int i = 0 ; i < split.length ; i++)
		{
			if(split[i].startsWith(">"))
			{
				name = split[i].substring(1);
				sequenceNames.add(name);
				if(!seq.equals(""))
				{
					sequences.add(seq);
					seq = "";
				}
				name = "";
			}
			else
			{
				seq += split[i].trim();
			}
		}
		if(!seq.equals(""))
		{
			sequences.add(seq);
		}
	}
	

	static class Alignment implements Serializable {
		/**
		 * 
		 */
		private static final long serialVersionUID = -4881397407402273139L;
		
		ArrayList<String> sequences = new ArrayList<String>();
		ArrayList<String> sequenceNames = new ArrayList<String>();

		public String toString() {
			String ret = "";
			for (int i = 0; i < sequences.size(); i++) {
				ret += ">" + sequenceNames.get(i) + "\n";
				ret += sequences.get(i) + "\n";
			}
			return ret;
		}
	}	
}