How to use

PatternScanMatch$PatternScanLocation

in

uk.ac.ebi.interpro.scan.model

  mappingFields.add(((PatternScanMatch.PatternScanLocation) location).getLevel().getTagNumber());
  mappingFields.add (((PatternScanMatch.PatternScanLocation) location).getCigarAlignment());
} else if (location instanceof PantherMatch.PantherLocation) {
  PantherMatch.PantherLocation pantherLocation = (PantherMatch.PantherLocation) location;

public Object clone() throws CloneNotSupportedException {
  final Set<PatternScanLocation> clonedLocations = new HashSet<PatternScanLocation>(this.getLocations().size());
  for (PatternScanLocation location : this.getLocations()) {
    clonedLocations.add((PatternScanLocation) location.clone());
  }
  return new PatternScanMatch(this.getSignature(), clonedLocations);
}

public Object clone() throws CloneNotSupportedException {
  return new PatternScanLocation(this.getStart(), this.getEnd(), this.getLevel(), this.getCigarAlignment());
}

/**
 * Returns sequence alignment.
 *
 * @return Sequence alignment.
 */
@XmlElement(required = true)
public String getAlignment() {
  if (cigarAlignment == null) {
    return null;
  }
  AlignmentEncoder encoder = new CigarAlignmentEncoder();
  return encoder.decode(getMatch().getProtein().getSequence(), cigarAlignment, getStart(), getEnd());
}

public PatternScanLocation(int start, int end, Level level, String cigarAlignment) {
  super(start, end);
  setLevel(level);
  setCigarAlignment(cigarAlignment);
}

  private PatternScanMatch buildMatch(Signature signature, ProSitePatternRawMatch rawMatch) {
    PatternScanMatch.PatternScanLocation location = new PatternScanMatch.PatternScanLocation(
        rawMatch.getLocationStart(),
        rawMatch.getLocationEnd(),
        rawMatch.getPatternLevel(),
        rawMatch.getCigarAlignment());
    return new PatternScanMatch(signature, rawMatch.getModelId(), Collections.singleton(location));
  }
}

public void setAlignment(String alignment) {
  AlignmentEncoder encoder = new CigarAlignmentEncoder();
  setCigarAlignment(encoder.encode(alignment));
}