AlignmentCountMapWritable.java

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/*******************************************************************************
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use these files 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.
 *
 * Copyright 2014 - Juan Pino, Aurelien Waite, William Byrne
 *******************************************************************************/

package uk.ac.cam.eng.extraction.hadoop.datatypes;

import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
import java.util.HashMap;

import org.apache.hadoop.io.Writable;
import org.apache.hadoop.io.file.tfile.Utils;

import uk.ac.cam.eng.extraction.Alignment;

public class AlignmentCountMapWritable extends
                HashMap<Alignment, Integer> implements Writable {

        private static final long serialVersionUID = 1L;

        public static final AlignmentCountMapWritable EMPTY = new AlignmentCountMapWritable() {

                private static final long serialVersionUID = 1L;

                public Integer put(Alignment key, Integer value) {
                        throw new UnsupportedOperationException();
                };
        };

        public AlignmentCountMapWritable() {

        }
        
        public AlignmentCountMapWritable(AlignmentCountMapWritable other){
                for(Entry<Alignment, Integer> entry : other.entrySet()){
                        put(new Alignment(entry.getKey()), entry.getValue());
                }
        }

        public void increment(AlignmentCountMapWritable newCounts) {
                for (Entry<Alignment, Integer> alignCount : newCounts
                                .entrySet()) {
                        Alignment key = alignCount.getKey();
                        if (containsKey(key)) {
                                put(key, get(key) + newCounts.get(key));
                        } else {
                                put(key, newCounts.get(key));
                        }
                }
        }
        
        public void merge(AlignmentCountMapWritable other) {
                int expectedSize = size() + other.size();
                putAll(other);
                if (expectedSize != size()) {
                        throw new RuntimeException("Merging twice the same alignment "
                                        + this + other);
                }
        }

        /*
         * (non-Javadoc)
         * 
         * @see org.apache.hadoop.io.Writable#write(java.io.DataOutput)
         */
        @Override
        public void write(DataOutput out) throws IOException {
                Utils.writeVInt(out, size());
                for (Alignment a : keySet()) {
                        a.write(out);
                        Utils.writeVInt(out, get(a));
                }
        }

        /*
         * (non-Javadoc)
         * 
         * @see org.apache.hadoop.io.Writable#readFields(java.io.DataInput)
         */
        @Override
        public void readFields(DataInput in) throws IOException {
                clear();
                int size = Utils.readVInt(in);
                for (int i = 0; i < size; ++i) {
                        Alignment a = new Alignment();
                        a.readFields(in);
                        int alignmentCount = Utils.readVInt(in);
                        put(a, alignmentCount);
                }
        }

}