inputStream = new FileInputStream(file);
Collection<DuplicateCode> result = parser.parse(inputStream, moduleName);
createLinkNames(result);
Set<FileAnnotation> warnings = Sets.newHashSet();
warnings.addAll(result);
ContextHashCode hashCode = new ContextHashCode();
for (FileAnnotation duplication : warnings) {
String fullPath = getFullPath(duplication);
long value = hashCode.create(fullPath,
duplication.getPrimaryLineNumber(), defaultEncoding);
duplication.setContextHashCode(value * 31 + (((DuplicateCode)duplication).getNumberOfLines()));
}
return warnings;