/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.io;

import jalview.datamodel.CigarParser;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.SortedMap;

import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;

public class BamFile extends AlignFile
{
  // SAM/BAM file reader
  private SamReader fileReader;

  // start position to read from
  private int start = -1;

  // end position to read to
  private int end = -1;

  // chromosome/contig to read
  private String chromosome = "";

  // first position in alignment
  private int alignmentStart = -1;

  /**
   * Creates a new BamFile object.
   */
  public BamFile()
  {
  }

  /**
   * Creates a new BamFile object.
   * 
   * @param inFile
   *          Name of file to read
   * @param sourceType
   *          Whether data source is file, url or other type of data source
   * 
   * @throws IOException
   */
  public BamFile(String inFile, DataSourceType sourceType)
          throws IOException
  {
    super(true, inFile, sourceType);
    final SamReaderFactory factory = SamReaderFactory.makeDefault()
            .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
                    SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
            .validationStringency(ValidationStringency.SILENT);
    fileReader = factory.open(new File(inFile));
  }

  /**
   * Creates a new BamFile object
   * 
   * @param source
   *          wrapper for datasource
   * @throws IOException
   */
  public BamFile(FileParse source) throws IOException
  {
    super(true, source);
    final SamReaderFactory factory = SamReaderFactory.makeDefault()
            .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
                    SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
            .validationStringency(ValidationStringency.SILENT);

    // File-based bam
    fileReader = factory.open(source.inFile);
  }
  
  @Override
  public String print(SequenceI[] seqs, boolean jvsuffix)
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public void parse()
  {
    // only actually parse if params are set
    if (chromosome != null && chromosome != "")
    {
      SAMRecordIterator it = fileReader.query(chromosome, start, end,
              false);
      CigarParser parser = new CigarParser('-');
      SortedMap<Integer, Integer> insertions = parser.getInsertions(it);
      it.close();

      it = fileReader.query(chromosome, start, end, false);
      while (it.hasNext())
      {
        SAMRecord rec = it.next();

        // set the alignment start to be start of first read (we assume reads
        // are sorted)
        if (alignmentStart == -1)
        {
          alignmentStart = rec.getAlignmentStart();
        }

        // make dataset sequence: start at 1, end at read length
        SequenceI seq = new Sequence(rec.getReadName(),
                rec.getReadString().toLowerCase());
        seq.setStart(1);
        seq.setEnd(rec.getReadLength());

        String newRead = parser.parseCigarToSequence(rec, insertions,
                alignmentStart, seq);

        // make alignment sequences
        SequenceI alsq = seq.deriveSequence();
        alsq.setSequence(newRead);

        // set start relative to soft clip; assume end is set by Sequence code
        alsq.setStart(rec.getStart() - rec.getUnclippedStart() + 1);
        seqs.add(alsq);
      }
    }
  }

  /**
   * Get the list of chromosomes or contigs from the file (listed in SQ entries
   * in BAM file header)
   * 
   * @return array of chromosome/contig strings
   */
  @Override
  public Object[] preprocess()
  {
    List<SAMSequenceRecord> refSeqs = fileReader.getFileHeader()
            .getSequenceDictionary().getSequences();
    List<String> chrs = new ArrayList<>();

    for (SAMSequenceRecord ref : refSeqs)
    {
      chrs.add(ref.getSequenceName());
    }
    return chrs.toArray();
  }

  public void setOptions(String chr, int s, int e)
  {
    chromosome = chr;
    start = s;
    end = e;
  }
}