Pair.java

/*
 * $Id: Pair.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program 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.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 */

package jaligner.formats;

import jaligner.Alignment;
import jaligner.util.Commons;

/**
 * <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.
 *
 * @author Ahmed Moustafa (ahmed@users.sf.net)
 */

public class Pair extends Format {
	
	/**
	 * Name width 
	 */
    private static final int NAME_WIDTH = 13;
	
    /**
     * Position width
     */
    private static final int POSITION_WIDTH = 6;
	
    /**
     * Sequence width
     */
    private static final int SEQUENCE_WIDTH = 50;
	
    /**
     * Space
     */
    private static final String BLANK = " ";
    
    /**
     * Constructor
     *
     */
    public Pair( ) {
    	super();
    	setId("Pair");
    }
	
	/**
	 * Formats an alignment object to the Pair_FORMAT format
	 * @param alignment alignment object to be formated
	 * @return string of the alignment pair-formatted
	 */
	public String format(Alignment alignment) {
		char[] sequence1 = alignment.getSequence1();
		char[] sequence2 = alignment.getSequence2();
		char[] markup = alignment.getMarkupLine();
		
		int length = sequence1.length > sequence2.length ? sequence2.length : sequence1.length;
		
		String name1 = adjustName(alignment.getName1());
		String name2 = adjustName(alignment.getName2());

		StringBuffer buffer = new StringBuffer ( );
		
		StringBuffer preMarkup = new StringBuffer ( );
		for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++) {
			preMarkup.append(BLANK);
		}
		
		int oldPosition1, position1 = 1 + alignment.getStart1();
		int oldPosition2, position2 = 1 + alignment.getStart2();
		
		char[] subsequence1;
		char[] subsequence2;
		char[] submarkup;
		int line;
		
		char c1, c2;
		
		for (int i = 0; i * SEQUENCE_WIDTH < length; i++) {
			
			oldPosition1 = position1;
			oldPosition2 = position2;
			
			line = ((i + 1) * SEQUENCE_WIDTH) < length ? (i + 1) * SEQUENCE_WIDTH: length;

			subsequence1 = new char[line - i * SEQUENCE_WIDTH];
			subsequence2 = new char[line - i * SEQUENCE_WIDTH];
			submarkup = new char[line - i * SEQUENCE_WIDTH];
		
			for (int j = i * SEQUENCE_WIDTH, k = 0; j < line; j++, k++) {
				subsequence1[k] = sequence1[j];
				subsequence2[k] = sequence2[j];
				submarkup[k] = markup[j];
				c1 = subsequence1[k];
				c2 = subsequence2[k];
				if (c1 == c2) {
					position1++;
					position2++;
				} else if (c1 == Alignment.GAP) {
					position2++;
				} else if (c2 == Alignment.GAP) {
					position1++;
				} else {
					position1++;
					position2++;
				}
			}

			buffer.append(name1);
			buffer.append(BLANK);
			buffer.append(adjustPosition(new Integer(oldPosition1).toString()));
			buffer.append(BLANK);
			buffer.append(subsequence1);
			buffer.append(BLANK);
			buffer.append(adjustPosition(new Integer(position1 - 1).toString()));
			buffer.append(Commons.getLineSeparator());
			
			buffer.append(preMarkup);
			buffer.append(submarkup);
			buffer.append(Commons.getLineSeparator());

			buffer.append(name2);
			buffer.append(BLANK);
			buffer.append(adjustPosition(new Integer(oldPosition2).toString()));
			buffer.append(BLANK);
			buffer.append(subsequence2);
			buffer.append(BLANK);
			buffer.append(adjustPosition(new Integer(position2 - 1).toString()));
			buffer.append(Commons.getLineSeparator());
			
			buffer.append(Commons.getLineSeparator());
		}
		return buffer.toString();
	}
	
	/**
	 * 
	 * @param name name to adjusted
	 * @return adjusted name
	 */
	private String adjustName(String name) {
		StringBuffer buffer = new StringBuffer ( );
		
		if (name.length() > NAME_WIDTH) {
			buffer.append(name.substring(0, NAME_WIDTH));
		} else {
			buffer.append(name);
			for (int j = buffer.length(); j < NAME_WIDTH; j++) {
				buffer.append (BLANK);
			}
		}
		return buffer.toString();
	}
	
	/**
	 * 
	 * @param position
	 * @return string
	 */
	private String adjustPosition(String position) {
		StringBuffer buffer1 = new StringBuffer( );
		StringBuffer buffer2 = new StringBuffer( );
		
		if (position.length() > POSITION_WIDTH) {
			buffer1.append(position.substring(position.length() - POSITION_WIDTH, position.length()));
		} else {
			buffer1.append(position);
		}
		
		for (int j = 0, n = POSITION_WIDTH - buffer1.length(); j < n; j++) {
			buffer2.append(BLANK);
		}
		
		buffer2.append(buffer1.toString());
		return buffer2.toString();
	}
}