/** Class for storing and working with sam formatted DNA sequence.
 *
 * Upon construction, only the String record is stored.
 * All querying of fields is done on demand, to save time.
 *
 */
public class SamRecord implements Record {

  private final String read;
  private String id = null;
  private int flag = -1;
  private String referenceName = null;
  private int pos = -1;
  private int mappingQuality = -1;
  private String cigar = null;
  private String mateReferenceName = null;
  private int matePosition = -1;
  private int templateLength = -1;
  private String sequence = null;
  private String quality = null;
  private String variableTerms = null;

  private final static String REPEAT_TERM = "ZS:Z:R";
  private final static String MATCH_TERM = "ZS:Z:NM";
  private final static String QUALITY_CHECK_TERM = "ZS:Z:QC";

  /** Simple constructor for the sam record
   * @param read full read
   */
  public SamRecord(String read) {
    this.read = read;
  }

  public String getRead() {
    return read;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public String getId() {
    if(id == null){
      id = XsamReadQueries.findID(read);
    }

    return id;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public int getFlag() throws NumberFormatException {
    if(flag == -1) {
      flag = Integer.parseInt(XsamReadQueries.findElement(read, 1));
    }
    return flag;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public String getReferenceName() {
    if(referenceName == null){
      referenceName = XsamReadQueries.findReferneceName(read);
    }

    return referenceName;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public int getPos() throws NumberFormatException{
    if(pos == -1){
      pos = Integer.parseInt(XsamReadQueries.findElement(read, 3));
    }

    return pos;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public int getMappingQuality() throws NumberFormatException {
    if(mappingQuality == -1){
      mappingQuality = Integer.parseInt(XsamReadQueries.findElement(read, 4));
    }

    return mappingQuality;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public String getCigar() {
    if(cigar == null){
      cigar = XsamReadQueries.findCigar(read);
    }

    return cigar;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public String getMateReferenceName() {
    if(mateReferenceName == null){
      mateReferenceName = XsamReadQueries.findElement(read, 6);
    }

    return mateReferenceName;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public int getMatePosition() throws NumberFormatException {
    if(matePosition == -1){
      matePosition = Integer.parseInt(XsamReadQueries.findElement(read, 7));
    }

    return matePosition;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public int getTemplateLength() throws NumberFormatException {
    if(templateLength == -1){
      templateLength = Integer.parseInt(XsamReadQueries.findElement(read, 8));
    }

    return templateLength;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public String getSequence() {
    if(sequence == null){
      sequence = XsamReadQueries.findBaseSequence(read);
    }

    return sequence;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public String getQuality() {
    if(quality == null){
      quality = XsamReadQueries.findElement(read, 10);
    }

    return quality;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public boolean isRepeat() {
    return read.contains(REPEAT_TERM);
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public boolean isMapped() {
    return !read.contains(MATCH_TERM);
  }


  /**
   * {@inheritDoc}
   */
  @Override
  public String getVariableTerms() {
    if(variableTerms == null){
      variableTerms = XsamReadQueries.findVariableRegionSequence(read);
    }

    return variableTerms;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public boolean isQualityFailed() {
    return read.contains(QUALITY_CHECK_TERM);
  }


  @Override
  public boolean equals(Object o) {
    if (this == o) return true;
    if (o == null || getClass() != o.getClass()) return false;
    SamRecord samRecord = (SamRecord) o;
    return Objects.equals(read, samRecord.read);
  }

  @Override
  public int hashCode() {
    return Objects.hash(read);
  }

  @Override
  public String toString() {
    return read;
  }
}