com.google.cloud.genomics.utils.Contig.java Source code

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Here is the source code for com.google.cloud.genomics.utils.Contig.java

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/*
 * Copyright (C) 2014 Google Inc.
 *
 * 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 com.google.cloud.genomics.utils;

import static com.google.common.base.Objects.equal;
import static com.google.common.collect.Lists.newArrayList;
import static java.util.Objects.hash;
import static java.util.Objects.requireNonNull;

import com.google.api.client.util.Preconditions;
import com.google.common.base.Function;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import com.google.genomics.v1.StreamReadsRequest;
import com.google.genomics.v1.StreamVariantsRequest;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;

/**
 * A Contig is a contiguous region of the genome.
 */
public class Contig implements Serializable {

    private static final long serialVersionUID = -1730387112193404207L;

    public final String referenceName;
    public final long start;
    public final long end;

    public Contig(String referenceName, long start, long end) {
        this.referenceName = requireNonNull(referenceName);
        this.start = start;
        this.end = end;
    }

    @Override
    public int hashCode() {
        return hash(referenceName, start, end);
    }

    @Override
    public boolean equals(Object obj) {
        if (!(obj instanceof Contig)) {
            return false;
        }
        Contig c = (Contig) obj;
        return equal(referenceName, c.referenceName) && equal(start, c.start) && equal(end, c.end);
    }

    @Override
    public String toString() {
        return referenceName + ':' + start + ':' + end;
    }

    /**
     * Parse the list of Contigs expressed in the string argument.
     *
     * The common use case is to parse the value of a command line parameter.
     *
     * @param contigsArgument - a string expressing the specified contiguous region(s) of the genome.
     *                          The format is chromosome:start:end[,chromosome:start:end]
     * @return a list of Contig objects
     */
    public static Iterable<Contig> parseContigsFromCommandLine(String contigsArgument) {
        return Iterables.transform(Splitter.on(",").split(contigsArgument), new Function<String, Contig>() {
            @Override
            public Contig apply(String contigString) {
                ArrayList<String> contigInfo = newArrayList(Splitter.on(":").split(contigString));
                Long start = Long.valueOf(contigInfo.get(1));
                Long end = Long.valueOf(contigInfo.get(2));
                Preconditions.checkArgument(start <= end, "Contig coordinates are incorrectly specified: start "
                        + start + " is greater than end " + end);
                return new Contig(contigInfo.get(0), start, end);
            }
        });
    }

    // The following methods have package scope and are helpers for ShardUtils. For sharded Contigs,
    // the ShardUtils methods should be used to ensure that shards are shuffled all together before
    // being returned to clients.
    List<Contig> getShards(long numberOfBasesPerShard) {
        double shardCount = (end - start) / (double) numberOfBasesPerShard;
        List<Contig> shards = Lists.newArrayList();
        for (int i = 0; i < shardCount; i++) {
            long shardStart = start + (i * numberOfBasesPerShard);
            long shardEnd = Math.min(end, shardStart + numberOfBasesPerShard);

            shards.add(new Contig(referenceName, shardStart, shardEnd));
        }
        return shards;
    }

    /**
     * Construct a StreamVariantsRequest for the Contig.
     * @param variantSetId
     * @return the request object
     */
    @Deprecated
    public StreamVariantsRequest getStreamVariantsRequest(String variantSetId) {
        return StreamVariantsRequest.newBuilder().setVariantSetId(variantSetId).setReferenceName(referenceName)
                .setStart(start).setEnd(end).build();
    }

    /**
     * Construct a StreamReadsRequest for the Contig.
     * @param readGroupSetId
     * @return the request object
     */
    @Deprecated
    public StreamReadsRequest getStreamReadsRequest(String readGroupSetId) {
        return StreamReadsRequest.newBuilder().setReadGroupSetId(readGroupSetId).setReferenceName(referenceName)
                .setStart(start).setEnd(end).build();
    }

    /**
     * Construct a StreamVariantsRequest for the Contig using a prototype using a prototype request.
     *
     * @param prototype A partially filled in request object.
     * @return the request object
     */
    public StreamVariantsRequest getStreamVariantsRequest(StreamVariantsRequest prototype) {
        return StreamVariantsRequest.newBuilder(prototype).setReferenceName(referenceName).setStart(start)
                .setEnd(end).build();
    }

    /**
     * Construct a StreamReadsRequest for the Contig using a prototype request.
     *
     * @param prototype A partially filled in request object.
     * @return the request object
     */
    public StreamReadsRequest getStreamReadsRequest(StreamReadsRequest prototype) {
        return StreamReadsRequest.newBuilder(prototype).setReferenceName(referenceName).setStart(start).setEnd(end)
                .build();
    }
}