/*
 * Copyright (C) 2009-2011 Institute for Computational Biomedicine,
 *                    Weill Medical College of Cornell University
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package edu.cornell.med.icb.goby.alignments;


import java.io.IOException;

/**
 * Returns NonAmbiguousAlignmentReader instances. Use this factory to filter out entries whose read matched in multiple
 * places in the reference sequence (as determined by the alignment parameters).
 *
 * @author Fabien Campagne
 *         Date: Apr 9, 2011
 *         Time: 4:37:26 PM
 */
public class NonAmbiguousAlignmentReaderFactory implements AlignmentReaderFactory {
    @Override
    public AlignmentReader createReader(String basename) throws IOException {
        return new NonAmbiguousAlignmentReader(basename);
    }

    @Override
    public AlignmentReader[] createReaderArray(int numElements) throws IOException {
        return new NonAmbiguousAlignmentReader[numElements];
    }

    @Override
    public AlignmentReader createReader(String basename, int startReferenceIndex,
                                        int startPosition, int endReferenceIndex, int endPosition) throws IOException {
        return new NonAmbiguousAlignmentReader(basename, startReferenceIndex, startPosition, endReferenceIndex, endPosition);
    }

    @Override
    public AlignmentReader createReader(String basename, GenomicRange range) throws IOException {
        if (range == null) {
            return createReader(basename);
        } else {
            return createReader(basename, range.startReferenceIndex, range.startPosition,
                    range.endReferenceIndex, range.endPosition);
        }
    }

    @Override
    public AlignmentReader createReader(String basename, long startOffset, long endOffset) throws IOException {
        return new NonAmbiguousAlignmentReader(startOffset, endOffset, basename);
    }

    @Override
    public FileSlice getSlice(String basename, GenomicRange range) throws IOException {
        return FileSlice.getSlice(this, basename, range);
    }
}