boa.aggregators.Aggregator.java Source code

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Here is the source code for boa.aggregators.Aggregator.java

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/*
 * Copyright 2015, Anthony Urso, Hridesh Rajan, Robert Dyer,
 *                 and Iowa State University of Science and Technology
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package boa.aggregators;

import java.io.IOException;

import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Reducer.Context;

import boa.functions.BoaCasts;
import boa.io.EmitKey;
import boa.io.EmitValue;

/**
 * The base class for all Boa aggregators.
 * 
 * @author anthonyu
 * @author rdyer
 */
public abstract class Aggregator {
    private long arg;
    @SuppressWarnings("rawtypes")
    private Context context;
    private EmitKey key;
    private boolean combining;

    /**
     * Construct an Aggregator.
     * 
     */
    public Aggregator() {
        // default constructor
    }

    /**
     * Construct an Aggregator.
     * 
     * @param arg
     *            A long (Boa int) containing the argument to the table
     * 
     */
    public Aggregator(final long arg) {
        this();

        this.arg = arg;
    }

    /**
     * Reset this aggregator for a new key.
     * 
     * @param key
     *            The {@link EmitKey} to aggregate for
     * 
     */
    public void start(final EmitKey key) {
        this.setKey(key);
    }

    public abstract void aggregate(String data, String metadata)
            throws IOException, InterruptedException, FinishedException;

    public void aggregate(final String data) throws IOException, InterruptedException, FinishedException {
        this.aggregate(data, null);
    }

    public void aggregate(final long data, final String metadata)
            throws IOException, InterruptedException, FinishedException {
        this.aggregate(BoaCasts.longToString(data), metadata);
    }

    public void aggregate(final long data) throws IOException, InterruptedException, FinishedException {
        this.aggregate(BoaCasts.longToString(data), null);
    }

    public void aggregate(final double data, final String metadata)
            throws IOException, InterruptedException, FinishedException {
        this.aggregate(BoaCasts.doubleToString(data), metadata);
    }

    public void aggregate(final double data) throws IOException, InterruptedException, FinishedException {
        this.aggregate(BoaCasts.doubleToString(data), null);
    }

    @SuppressWarnings("unchecked")
    protected void collect(final String data, final String metadata) throws IOException, InterruptedException {
        if (this.combining)
            this.getContext().write(this.getKey(), new EmitValue(data, metadata));
        else if (metadata != null)
            this.getContext().write(new Text(this.getKey() + " = " + data + " weight " + metadata),
                    NullWritable.get());
        else
            this.getContext().write(new Text(this.getKey() + " = " + data), NullWritable.get());
    }

    protected void collect(final String data) throws IOException, InterruptedException {
        this.collect(data, null);
    }

    @SuppressWarnings("unchecked")
    protected void collect(final long data, final String metadata) throws IOException, InterruptedException {
        this.collect(BoaCasts.longToString(data), metadata);
    }

    protected void collect(final long data) throws IOException, InterruptedException {
        this.collect(BoaCasts.longToString(data), null);
    }

    @SuppressWarnings("unchecked")
    protected void collect(final double data, final String metadata) throws IOException, InterruptedException {
        this.collect(BoaCasts.doubleToString(data), metadata);
    }

    protected void collect(final double data) throws IOException, InterruptedException {
        this.collect(BoaCasts.doubleToString(data), null);
    }

    public void finish() throws IOException, InterruptedException {
        // do nothing by default
    }

    public long getArg() {
        return this.arg;
    }

    public void setContext(@SuppressWarnings("rawtypes") final Context context) {
        this.context = context;
    }

    public boolean isCombining() {
        return this.combining;
    }

    public void setCombining(final boolean combining) {
        this.combining = combining;
    }

    @SuppressWarnings("rawtypes")
    public Context getContext() {
        return this.context;
    }

    public void setKey(final EmitKey key) {
        this.key = key;
    }

    public EmitKey getKey() {
        return this.key;
    }
}