htsjdk.samtools.SAMFileSpan Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 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.samtools;
/**
* A interface representing a collection of (possibly) discontinuous segments in the
* BAM file, possibly representing the results of an index query.
*/
public interface SAMFileSpan extends Cloneable {
/**
* Gets a pointer over the data immediately following this span.
* @return The a pointer to data immediately following this span.
*/
public SAMFileSpan getContentsFollowing();
/**
* Remove all pointers in this file span before the given file span starts.
* @param fileSpan The filespan before which to eliminate.
* @return The portion of the chunk list after the given chunk.
*/
public SAMFileSpan removeContentsBefore(final SAMFileSpan fileSpan);
/**
* Does this file span point to any data, or is it completely empty?
* @return True if the file span is empty, false otherwise.
*/
public boolean isEmpty();
}