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• 1.5.0
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• CharactersBlock.java

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lphy.base.parser.nexus.CharactersBlock Maven / Gradle / Ivy

/*
 * Copyright (C) 2014 Tim Vaughan 
 *
 * 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 3 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, see .
 */

package lphy.base.parser.nexus;

import lphy.base.evolution.alignment.SimpleAlignment;

import java.util.ArrayList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;

/**
 * A Nexus block containing a sequence alignment.  Note that this is preferred
 * over the often-used "data" block by Maddison et al.
 *
 * @author Tim Vaughan <[email protected]>
 */
public class CharactersBlock extends NexusBlock {

    private final SimpleAlignment alignment;

    public CharactersBlock(SimpleAlignment alignment) {
        this.alignment = alignment;
    }
    
    @Override
    public String getBlockName() {
        return "characters";
    }

    @Override
    public List getBlockLines() {
        List lines = new ArrayList<>();
        
        lines.add("dimensions nchar=" + alignment.nchar());
        
        // Assumes BEAST sequence data types map directly
        // onto nexus data types.  No doubt a bad idea in general...
        lines.add("format datatype=" + alignment.getSequenceTypeStr());
        
        StringBuilder matrix = new StringBuilder("matrix ");
        for (int i=0; i