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• lphy-base
• 1.5.0
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• TaxaBlock.java

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lphy.base.parser.nexus.TaxaBlock 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 java.util.ArrayList;
import java.util.List;

/**
 * Nexus Taxa block.
 *
 * @author Tim Vaughan <[email protected]>
 */
public class TaxaBlock extends NexusBlock {
    
    private final String[] taxa;

    public TaxaBlock(String[] taxa) {
        this.taxa = taxa;
    }

    @Override
    public String getBlockName() {
        return "taxa";
    }

    @Override
    public List getBlockLines() {
        List lines = new ArrayList<>();

        int ntax = taxa.length;

        lines.add("dimensions ntax=" + ntax);

        StringBuilder taxLabels = new StringBuilder("taxlabels");
        for (int i=0; i