/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 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 org.broad.igv.sam;

import org.broad.igv.feature.genome.Genome;

/**
 * Created by jrobinso on 9/22/15.
 */
public interface AlignmentBlock {

    boolean contains(int position);

    int getBasesLength();

    /**
     * Offset into read sequence
     */
    int getBasesOffset();

    int getLength();

    byte getBase(int offset);

    ByteSubarray getBases();

    int getStart();

    byte getQuality(int offset);

    ByteSubarray getQualities();

    int getEnd();

    boolean isSoftClip();

    boolean hasBases();

    void setPixelRange(int s, int e);

    boolean containsPixel(int x) ;

    default int getPadding() {
        return 0;
    }

    char getCigarOperator();

}
