htsjdk.tribble.index.ChrIndex Maven / Gradle / Ivy

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/*
 * The MIT License
 *
 * Copyright (c) 2013 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package htsjdk.tribble.index;

import htsjdk.tribble.util.LittleEndianInputStream;
import htsjdk.tribble.util.LittleEndianOutputStream;

import java.io.IOException;
import java.util.List;

/**
 * Represents an index on a specific chromosome
 */

public interface ChrIndex {

    public String getName();

    /**
     * @return all blocks in ChrIndex
     */
    List getBlocks();

    /**
     * @param start the start position, one based
     * @param end   the end position, one based
     * @return a list of blocks that include the region defined from start to stop.  Can never return null
     */
    List getBlocks(int start, int end);

    void write(LittleEndianOutputStream dos) throws IOException;

    void read(LittleEndianInputStream dis) throws IOException;
}