/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */

/*
 * Created on 2005-08-03
 */
package org.biojava.bio.alignment;

import java.util.List;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.db.SequenceDB;
import org.biojava.bio.symbol.Alignment;
import org.biojava.bio.symbol.SymbolList;

/**
 * This Interface provides methods for the alignment of bio-sequences.
 *
 * @author Andreas Dr&auml;ger <andreas.draeger@uni-tuebingen.de>
 * @author Mark Schreiber
 */
public abstract class SequenceAlignment {
	/**
	 * @return a string representation of the alignment
	 * @throws BioException
	 */
	public abstract String getAlignmentString() throws Exception;

	/**
	 * @param source
	 *          a SequenceIterator containing a set of sequences to be aligned
	 *          with
	 * @param subjectDB
	 *          the SequenceDB containing another set of sequences.
	 * @return a list containing the results of all single alignments performed by
	 *         this method.
	 * @throws NoSuchElementException
	 * @throws Exception
	 */
	public abstract List alignAll(SequenceIterator source, SequenceDB subjectDB)
	    throws Exception;

	/**
	 * Performs a pairwise sequence alignment of the two given sequences.
	 *
	 * @param query
	 * @param subject
	 * @return score of the alignment or the distance.
	 * @throws Exception
	 */
	public abstract int pairwiseAlignment(SymbolList query, SymbolList subject)
	    throws Exception;

	/**
	 * This method also performs a sequence alignment of the two given sequences
	 * but it returns an Alignment object instead of the score.
	 *
	 * @param query
	 * @param subject
	 * @return Alignment
	 */
	public abstract Alignment getAlignment(SymbolList query, SymbolList subject)
	    throws Exception;

	/**
	 * This method provides a BLAST-like formated alignment from the given
	 * <code>String</code>s, in which the sequence coordinates and the
	 * information "Query" or "Target", respectively is added to each line. Each
	 * line contains 60 sequence characters including the gap symbols plus the
	 * meta information. There is one white line between two pairs of sequences.
	 *
	 * @param queryName
	 *          name of the query sequence
	 * @param targetName
	 *          name of the target sequence
	 * @param align
	 *          a <code>String</code>-array, where the index 0 is the query
	 *          sequence and index 1 the target sequence (for instance
	 *          <code>new String[] {myQuerySequence.seqString(), myTargetSequence.seqString()}</code>)
	 * @param path
	 *          the "path", that means a String containing white spaces and pipe
	 *          ("|") symbols, which makes matches visible. The two strings in
	 *          <code>align</code> have to have the same length and also the
	 *          same length than this <code>path</code>.
	 * @param queryStart
	 *          the start position in the query, where the alignment starts. For
	 *          example zero for normal Needleman-Wunsch-Alignments.
	 * @param queryEnd
	 *          the end position, that means the sequence coordinate, which is the
	 *          last symbol of the query sequence. Counting starts at zero!
	 * @param queryLength
	 *          The length of the query sequence without gaps.
	 * @param targetStart
	 *          These are all the same for the target. Have a look at these above.
	 * @param targetEnd
	 * @param targetLength
	 * @param editdistance
	 * @param time
	 *          The time in milliseconds, which was needed to generate the
	 *          alignment.
	 * @return formated String.
	 */
	public static StringBuffer formatOutput(String queryName, String targetName,
	    String[] align, String path, int queryStart, int queryEnd,
	    long queryLength, int targetStart, int targetEnd, long targetLength,
	    int editdistance, long time) {
		final String newLine = System.getProperty("line.separator");
		StringBuffer output = new StringBuffer(newLine);
		output.append(" Time (ms):\t");
		output.append(time);
		output.append(newLine);
		output.append(" Length:\t");
		output.append(align[0].length());
		output.append(newLine);
		output.append("  Score:\t" + (-1) * editdistance);
		output.append(newLine);
		output.append("  Query:\t");
		output.append(queryName);
		output.append(",\tLength:\t");
		output.append(queryLength);
		output.append(newLine);
		output.append("  Target:\t");
		output.append(targetName);
		output.append(",\tLength:\t");
		output.append(targetLength);
		output.append(newLine);
		output.append(newLine);

		int currline = Math.min(60, align[0].length()), i, j, k, l;
		// counts the absolute position within the String
		String space = "  ", kspace = "", jspace = "";
		for (k = 0; k < new Integer(Math.max(queryEnd, targetEnd)).toString()
		    .length(); k++)
			space += " ";
		for (k = new Integer(queryStart + 1).toString().length(); k <= new Integer(
		    Math.max(queryEnd, targetEnd)).toString().length(); k++)
			kspace += " ";
		for (k = new Integer(targetStart + 1).toString().length(); k <= new Integer(
		    Math.max(queryEnd, targetEnd)).toString().length(); k++)
			jspace += " ";

		i = k = queryStart;
		j = l = targetStart;
		output.append(newLine);
		output.append("Query:\t");
		output.append(kspace);
		output.append((k + 1));
		output.append(' ');
		for (i = currline - Math.min(60, align[0].length()); i < currline; i++) {
			if ((align[0].charAt(i) != '-') && (align[0].charAt(i) != '~')) k++;
			if ((align[1].charAt(i) != '-') && (align[1].charAt(i) != '~')) j++;
		}
		output.append(align[0].substring(0, currline));
		output.append(' ');
		output.append(k);
		output.append(' ');
		output.append(newLine);
		output.append("        ");
		output.append(space);
		output.append(path.substring(0, currline));
		output.append(' ');
		output.append(newLine);
		output.append("Target:\t");
		output.append(jspace);
		output.append((l + 1));
		output.append(' ');
		output.append(align[1].substring(0, currline));
		output.append(' ');
		output.append(j);
		output.append(' ');
		output.append(newLine);

		for (; currline + 60 < path.length(); currline += 60) {
			l = Math.min(j + 1, targetEnd);
			kspace = jspace = "";
			for (int n = new Integer(k + 1).toString().length() - 1; n < new Integer(
			    Math.max(queryEnd, targetEnd)).toString().length(); n++)
				kspace += " ";
			for (int n = new Integer(j).toString().length() - 1; n < new Integer(Math
			    .max(queryEnd, targetEnd)).toString().length(); n++)
				jspace += " ";
			output.append(' ');
			output.append(newLine);
			output.append("Query:\t");
			output.append(kspace);
			output.append(Math.min(k + 1, queryEnd));
			output.append(' ');
			for (i = currline; i < currline + 60; i++) {
				if ((align[0].charAt(i) != '-') && (align[0].charAt(i) != '~')) k++;
				if ((align[1].charAt(i) != '-') && (align[1].charAt(i) != '~')) j++;
			}
			output.append(align[0].substring(currline, currline + 60));
			output.append(' ');
			output.append(k);
			output.append(' ');
			output.append(newLine);
			output.append("        ");
			output.append(space);
			output.append(path.substring(currline, currline + 60));
			output.append(' ');
			output.append(newLine);
			output.append("Target:\t");
			output.append(jspace);
			output.append(l);
			output.append(' ');
			output.append(align[1].substring(currline, currline + 60));
			output.append(' ');
			output.append(j);
			output.append(' ');
			output.append(newLine);
		}
		align[0] += " " + queryEnd;
		align[1] += " " + targetEnd;
		if (currline + 1 < path.length()) {
			kspace = jspace = "";
			for (int n = new Integer(k).toString().length() - 1; n < new Integer(Math
			    .max(queryEnd, targetEnd)).toString().length(); n++)
				kspace += " ";
			for (int n = new Integer(j).toString().length() - 1; n < new Integer(Math
			    .max(queryEnd, targetEnd)).toString().length(); n++)
				jspace += " ";
			output.append(' ');
			output.append(newLine);
			output.append("Query:\t");
			output.append(kspace);
			output.append(Math.min(k + 1, queryEnd));
			output.append(' ');
			output.append(align[0].substring(currline, align[0].length()));
			output.append(' ');
			output.append(newLine);
			output.append("        ");
			output.append(space);
			output.append(path.substring(currline, path.length()));
			output.append(' ');
			output.append(newLine);
			output.append("Target:\t");
			output.append(jspace);
			output.append(Math.min(j + 1, targetEnd));
			output.append(' ');
			output.append(align[1].substring(currline, align[1].length()));
			output.append(newLine);
		}
		output.append(newLine);
		return output;
	}

}