/*
* CharSetAlignment.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evolution.alignment;
import dr.app.beauti.util.NexusApplicationImporter;
import dr.evolution.sequence.Sequence;
/**
* Created by IntelliJ IDEA.
* User: alexei
* Date: 1/08/11
* Time: 8:04 PM
* To change this template use File | Settings | File Templates.
*/
public class CharSetAlignment extends SimpleAlignment {
public CharSetAlignment(NexusApplicationImporter.CharSet charset, Alignment parentAlignment) {
setId(charset.getName());
for (int i = 0; i < parentAlignment.getSequenceCount(); i++) {
Sequence sequence = parentAlignment.getSequence(i);
String sequenceString = parentAlignment.getAlignedSequenceString(i);
String filteredSequence = filter(charset, sequenceString);
addSequence(new Sequence(sequence.getTaxon(), filteredSequence));
}
setDataType(parentAlignment.getDataType());
}
private String filter(NexusApplicationImporter.CharSet charset, String sequenceString) {
StringBuilder filtered = new StringBuilder();
for (NexusApplicationImporter.CharSetBlock block : charset.getBlocks()) {
int toSite = block.getToSite();
if (toSite <= 0) {
toSite = sequenceString.length();
}
for (int i = block.getFromSite(); i <= toSite; i += block.getEvery()) {
// the -1 comes from the fact that charsets are indexed from 1 whereas strings are indexed from 0
filtered.append(sequenceString.charAt(i - 1));
}
}
return filtered.toString();
}
}