/*
* GapUtils.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 java.util.List;
/**
* @author Alexei Drummond
*
* @version $Id: GapUtils.java,v 1.3 2005/04/20 21:26:19 rambaut Exp $
*/
public class GapUtils {
/**
* Adds Integer objects to the given list representing the sizes of the gaps found in the given alignment.
* Note -- it only handles pairwise alignments
* @param alignment a pairwise alignment
* @param gaps a list in which the gap sizes will be added
*/
public static void getGapSizes(Alignment alignment, List gaps) {
int stateCount = alignment.getDataType().getStateCount();
int gapStart = Integer.MAX_VALUE;
for (int i = 0; i < alignment.getSiteCount(); i++) {
int x = alignment.getState(0,i);
int y = alignment.getState(1,i);
if (y < stateCount && x < stateCount) {
// no gap
if (gapStart < i) {
gaps.add(new Integer(i-gapStart));
gapStart = Integer.MAX_VALUE;
}
} else {
// gap
if (gapStart > i) gapStart = i;
}
}
}
}