/*
 * 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.SequenceI;

import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.Iterator;

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

public class BamFile extends AlignFile
{

  SamReader fileReader;

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

  /**
   * Creates a new BamFile object.
   * 
   * @param inFile
   *          DOCUMENT ME!
   * @param sourceType
   *          DOCUMENT ME!
   * 
   * @throws IOException
   *           DOCUMENT ME!
   */
  public BamFile(String inFile, DataSourceType sourceType)
          throws IOException
  {
    super(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));
  }

  public BamFile(FileParse source) throws IOException
  {
    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);
    parse();
  }
  
  @Override
  public String print(SequenceI[] seqs, boolean jvsuffix)
  {
    // TODO Auto-generated method stub
    return null;
  }

  @Override
  public void parse() throws IOException
  {
    SequenceI seq = null;
    SAMRecordIterator it = fileReader.iterator();
    while (it.hasNext())
    {
      SAMRecord rec = it.next();
      String read = rec.getReadString();
      int start = rec.getStart();
      int end = rec.getEnd();

      Iterator<CigarElement> cit = rec.getCigar().getCigarElements()
              .iterator();

      seq = parseId(rec.getReadName());
      String cigarredRead = parseCigarToSequence(read, cit, '-');
      seq.setSequence(cigarredRead);
      seq.setStart(start);
      seq.setEnd(end);
      seqs.addElement(seq);
    }

  }

  /**
   * Apply the CIGAR string to a read sequence and return the updated read
   * 
   * @param read
   *          the read to update
   * @param it
   *          iterator over cigar elements
   * @param gapChar
   *          gap character to use
   * @return string representing read with gaps, clipping etc applied
   */
  private String parseCigarToSequence(String read,
          Iterator<CigarElement> it, char gapChar)
  {
    StringBuilder newRead = new StringBuilder();
    int next = 0;

    while (it.hasNext())
    {
      CigarElement el = it.next();
      int length = el.getLength();
      switch (el.getOperator())
      {
      case M:
        // matched residues
        newRead.append(read.substring(next, next + length - 1));
        next += length;
        break;
      case N: // intron in RNA
      case D: // deletion
        // add gaps
        char[] gaps = new char[length];
        Arrays.fill(gaps, gapChar);
        newRead.append(gaps);
        break;
      case S:
        // soft clipping - just skip this bit of the read
        // do nothing
        next += length;
        break;
      case I:
        // add gaps to the reference sequence, which we know nothing about just
        // now
        // TODO
        newRead.append(read.substring(next, next + length - 1));
        break;
      case H:
        // hard clipping - this stretch will not appear in the read
        break;
      default:
        // P, X EQ don't know what to do with these
        break;
      }

    }
    return newRead.toString();
  }

}