/*
* $Id: CLUSTAL.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;
/**
* CLUSTAL format.
* Example:
* <pre>
* <small>
* CLUSTAL_FORMAT W(1.60) multiple sequence alignment
*
*
* JC2395 NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
* KPEL_DROME MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
* FASA_MOUSE NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
*
*
* JC2395 -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
* KPEL_DROME -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
* FASA_MOUSE -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
*
*
* JC2395 IAEEIQAM
* KPEL_DROME AMRLIKDY
* FASA_MOUSE TLDKFQDM
* </small>
* </pre>
*
* @author Ahmed Moustafa (ahmed@users.sf.net)
*/
public class CLUSTAL extends Format {
/**
* Name width
*/
private static final int NAME_WIDTH = 36;
/**
* Sequence width
*/
private static final int SEQUENCE_WIDTH = 50;
/**
* CLUSTAL header
*/
private static final String HEADER = "CLUSTAL_FORMAT W(1.60) multiple sequence alignment\n\n";
/**
* Constructor
*/
public CLUSTAL() {
super( );
setId("CLUSTAL");
}
/**
* Returns CLUSTAL format
* @param names array of the names of the sequences.
* @param sequences array of the sequences
*/
public String format(String[] names, String[] sequences) {
StringBuffer buffer = new StringBuffer (HEADER);
int maxSequenceLength = 0;
for (int i = 0; i < sequences.length; i++) {
if (sequences[i].length() > maxSequenceLength) {
maxSequenceLength = sequences[i].length();
}
}
for (int i = 0; i * SEQUENCE_WIDTH < maxSequenceLength; i++) {
for (int j = 0; j < sequences.length; j++) {
buffer.append( NAME_WIDTH <= names[j].length() ? names[j].substring(0, NAME_WIDTH - 1) : names[j] );
for (int k = names[j].length(); k < NAME_WIDTH; k++) {
buffer.append(" ");
}
if (names[j].length() >= NAME_WIDTH) {
buffer.append(" ");
}
buffer.append(sequences[j].substring(i * SEQUENCE_WIDTH, ((i + 1) * SEQUENCE_WIDTH) < sequences[j].length() ? (i + 1) * SEQUENCE_WIDTH: sequences[j].length()));
if (j < sequences.length) {
buffer.append("\n");
}
}
if ((i + 1) * SEQUENCE_WIDTH < maxSequenceLength) {
buffer.append("\n\n");
}
}
return buffer.toString();
}
/**
* Returns CLUSTAL format of the alignment
* @param alignment ({@link Alignment})
* @return CLUSTAL format of the alignment
*/
public String format (Alignment alignment) {
String[] sequences = {new String(alignment.getSequence1()), new String(alignment.getSequence2())};
String[] names = {alignment.getName1(), alignment.getName2()};
return format (names, sequences);
}
}