/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */

package org.broad.igv.sam.reader;

import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.CloseableIterator;
import org.broad.igv.sam.Alignment;
import org.broad.igv.util.ResourceLocator;

import java.io.IOException;
import java.util.*;

/**
 * Poorly named class.  Created to wrap a list of sam files (1 per chromosome) as a single logical file
 */

public class SamListReader implements AlignmentQueryReader {

    SAMFileHeader header;

    Map<String, ResourceLocator> locators;
    Map<String, AlignmentQueryReader> readers;

    public SamListReader(Map<String, ResourceLocator> locators) {
        this.locators = locators;
        readers = new HashMap(locators.size());
    }

    public void close() throws IOException {
        for (AlignmentQueryReader reader : readers.values()) {
            reader.close();
        }
        readers.clear();
    }

    public SAMFileHeader getHeader() {
        if (locators == null || locators.size() == 0) {
            return null;
        }
        if (header == null) {
            // Any header will do, see if we have one
            if (readers.size() == 0) {
                Map.Entry<String, ResourceLocator> tmp = locators.entrySet().iterator().next();
                AlignmentQueryReader firstReader = SamQueryReaderFactory.getReader(tmp.getValue());
                readers.put(tmp.getKey(), firstReader);
            }
            header = (readers.values().iterator().next()).getHeader();
        }
        return header;
    }

    public Set<String> getSequenceNames() {
        SAMFileHeader header = getHeader();
        if (header == null) {
            return null;
        }
        Set<String> seqNames = new HashSet();
        List<SAMSequenceRecord> records = header.getSequenceDictionary().getSequences();
        if (records.size() > 0) {
            for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) {
                String chr = rec.getSequenceName();
                seqNames.add(chr);
            }
        }
        return seqNames;
    }

    public CloseableIterator<Alignment> iterator() {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public CloseableIterator<Alignment> query(String chr, int start, int end, boolean contained) {
        AlignmentQueryReader reader = readers.get(chr);
        if (reader == null) {
            ResourceLocator locator = locators.get(chr);
            if (locator == null) {
                // TODO -- return empty iterator?
                return null;
            }
            reader = SamQueryReaderFactory.getReader(locator);
        }
        return reader.query(chr, start, end, contained);
    }

    public boolean hasIndex() {
        // TODO -- test one of the readers
        return true;
    }
}
