/*
* PartitionDataList.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.app.bss;
import dr.evolution.alignment.SimpleAlignment;
import dr.evolution.util.Taxa;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.LinkedList;
/**
* @author Filip Bielejec
* @version $Id$
*/
@SuppressWarnings("serial")
public class PartitionDataList extends ArrayList<PartitionData> implements Serializable {
public int simulationsCount = 1;
public boolean useParallel = false;
public boolean outputAncestralSequences = false;
public SimpleAlignment.OutputType outputFormat = SimpleAlignment.OutputType.FASTA;
//List of all Taxa displayed in Taxa Panel
public Taxa allTaxa = new Taxa();
public LinkedList<TreesTableRecord> recordsList = new LinkedList<TreesTableRecord>();
// do not serialize this two
public transient boolean setSeed = false;
public transient long startingSeed;
public PartitionDataList() {
super();
startingSeed = System.currentTimeMillis();
}// END: Constructor
}// END:class