/**
* Search through a map of id-IndexElement mapping using the a element find the id when the index
* element fall into the same range.
*
* @param element a index element
* @param mappings id-indexelement mappings.
* @return String id
*/
private String searchForId(IndexElement element, Map<String, IndexElement> mappings) {
String id = null;
for (Map.Entry<String, IndexElement> entry : mappings.entrySet()) {
IndexElement identElement = entry.getValue();
if (identElement.getStart() <= element.getStart()
&& identElement.getStop() >= element.getStop()) {
id = entry.getKey();
break;
}
}
return id;
}
/**
* Find the id from xml string based indexElement's range.
*
* @param indexElement index element.
* @param pattern This pattern should only match once.
* @return String id or accession.
*/
private String getIDByPattern(IndexElement indexElement, Pattern pattern, boolean quickMatch) {
String id = null;
// first get the XML string (only the first bit) from which to extract the ID
long start = indexElement.getStart();
long stop = quickMatch ? start + XML_CHAR_INCREMENT : indexElement.getStop();
String xml = indexer.getXmlSnippet(start, stop);
// then apply the regex pattern to find the ID
Matcher m = pattern.matcher(xml);
if (m.find()) {
id = m.group(1);
}
return id;
}