/*
* 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.feature.tribble;
import htsjdk.tribble.Feature;
import htsjdk.tribble.index.Index;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
/**
* Interface to replace the Tribble equivalent. Returns plain "Iterator" rather than "CloseableIterator". A wrapper
* implementation is provided that handles closing the tribble resource.
*
* NOTE: IGV classes should use this interface, rather than the Tribble FeatureReader.
*
* @author jrobinso
* Date: 5/8/13
* Time: 10:55 AM
*/
public interface IGVFeatureReader {
public Iterator<Feature> query(final String chr, final int start, final int end) throws IOException;
public Iterator<Feature> iterator() throws IOException;
public List<String> getSequenceNames();
public Object getHeader();
}