edu.berkeley.compbio.phyloutils.TraditionalTaxonMerger.java Source code

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Here is the source code for edu.berkeley.compbio.phyloutils.TraditionalTaxonMerger.java

Source

/*
 * Copyright (c) 2006-2013  David Soergel  <dev@davidsoergel.com>
 * Licensed under the Apache License, Version 2.0
 * http://www.apache.org/licenses/LICENSE-2.0
 */

package edu.berkeley.compbio.phyloutils;

import org.apache.commons.lang.NotImplementedException;
import org.apache.log4j.Logger;

import java.io.Serializable;
import java.util.Collection;
import java.util.Map;
import java.util.Set;

/**
 * @author <a href="mailto:dev@davidsoergel.com">David Soergel</a>
 * @version $Id$
 */
public class TraditionalTaxonMerger {
    // ------------------------------ FIELDS ------------------------------

    private static final Logger logger = Logger.getLogger(TraditionalTaxonMerger.class);

    public static <T extends Serializable> Map<T, Set<T>> merge(Collection<T> leafIds,
            TaxonomyService<T> basePhylogeny, String levelName) {
        throw new NotImplementedException();
        /*
        Map<T, Set<T>> theTaxonsetsByTaxid = new HashMap<T, Set<T>>();
            
        for (T id : leafIds)
           {
           T requestedLevelId = basePhylogeny.nearestAncestorAtRank(levelName);
           //T knownId = basePhylogeny.nearestAncestorWithBranchLength(id);
           Set<T> currentTaxonset = theTaxonsetsByTaxid.get(requestedLevelId);
           if (currentTaxonset == null)
        {
        currentTaxonset = new HashSet<T>();
        theTaxonsetsByTaxid.put(requestedLevelId, currentTaxonset);
        }
            
           currentTaxonset.add(id);
           }
            
        return theTaxonsetsByTaxid;
        */
    }
}