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

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

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/*
 * 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 com.davidsoergel.trees.AbstractRootedPhylogeny;
import com.davidsoergel.trees.NoSuchNodeException;
import com.davidsoergel.trees.RootedPhylogeny;
import com.davidsoergel.trees.TreeException;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;

/**
 * Reads an environment file in the UniFrac format (http://bmf2.colorado.edu/unifrac/tutorial.psp), matching the taxon
 * names against nodes in the given tree, and provides the resulting communities as weighted RootedPhylogenies.
 *
 * @author <a href="mailto:dev@davidsoergel.com">David Soergel</a>
 * @version $Id$
 */
public class EnvironmentParser {

    public static Collection<RootedPhylogeny<String>> read(InputStream is, RootedPhylogeny<String> tree)
            throws IOException, TreeException, NoSuchNodeException {
        BufferedReader r = new BufferedReader(new InputStreamReader(is));

        Map<String, Multiset<String>> environmentCounts = new HashMap<String, Multiset<String>>();

        String line;
        while ((line = r.readLine()) != null) {
            String[] tokens = line.split(" ");
            Multiset<String> env = environmentCounts.get(tokens[1]);
            if (env == null) {
                env = HashMultiset.create();
                environmentCounts.put(tokens[1], env);
            }
            env.add(tokens[0], Integer.parseInt(tokens[2]));
        }

        Set<RootedPhylogeny<String>> result = new HashSet<RootedPhylogeny<String>>();
        for (Map.Entry<String, Multiset<String>> entry : environmentCounts.entrySet()) {
            String name = entry.getKey();
            Multiset<String> ids = entry.getValue();
            RootedPhylogeny<String> subtree = tree.extractTreeWithLeafIDs(ids.elementSet(), false, false,
                    AbstractRootedPhylogeny.MutualExclusionResolutionMode.EXCEPTION);
            subtree.setPayload(name);
            subtree.setLeafWeights(ids);
            result.add(subtree);
        }
        return result;
    }
}