list/src/main/java/alg/XML_processing.java

package alg;

import static data.Enums.solar.SolarFilters.*;

import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.util.*;
import java.util.concurrent.ForkJoinPool;

import javax.xml.namespace.QName;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.*;

import org.apache.logging.log4j.LogManager;

import data.*;
import gui.ValidationUtil;

public class XML_processing {
	public final static org.apache.logging.log4j.Logger logger = LogManager.getLogger(XML_processing.class);

	// public static void processCorpus(Statistics stats) {
	// 	// we can preset the list's size, so there won't be a need to resize it
	// 	List<Sentence> corpus = new ArrayList<>(Settings.CORPUS_SENTENCE_LIMIT);
	//
	// 	int i = 0;
	// 	for (File f : Settings.corpus) {
	// 		i++;
	// 		readXML(f.toString(), stats);
	// 	}
	// }

	// public static void readXML(String path, Statistics stats) {
	// 	if (stats.getCorpusType() == CorpusType.GIGAFIDA) {
	// 		readXMLGigafida(path, stats);
	// 	} else if (stats.getCorpusType() == CorpusType.GOS) {
	// 		readXMLGos(path, stats);
	// 	} else if (stats.getCorpusType() == CorpusType.SOLAR) {
	// 		readXMLSolar(path, stats);
	// 	}
	// }

	public static void readXML(String path, StatisticsNew stats) {
		if (stats.getCorpus().getCorpusType() == CorpusType.GIGAFIDA
				|| stats.getCorpus().getCorpusType() == CorpusType.CCKRES) {
			readXMLGigafida(path, stats);
		} else if (stats.getCorpus().getCorpusType() == CorpusType.GOS) {
			readXMLGos(path, stats);
		} else if (stats.getCorpus().getCorpusType() == CorpusType.SOLAR) {
			readXMLSolar(path, stats);
		}
	}

	/**
	 * Reads and returns the value of a passed header tag or an empty string.
	 * E.g. title tag, for discerning the corpus' type.
	 * Notice: returns only the value of the first occurrence of a given tag name.
	 */
	public static String readXMLHeaderTag(String path, String tag) {
		XMLInputFactory factory = XMLInputFactory.newInstance();
		XMLEventReader eventReader = null;

		try {
			eventReader = factory.createXMLEventReader(new FileInputStream(path));
			while (eventReader.hasNext()) {
				XMLEvent xmlEvent = eventReader.nextEvent();
				if (xmlEvent.isStartElement()) {
					StartElement startElement = xmlEvent.asStartElement();
					String var = startElement.getName().getLocalPart();

					if (var.equalsIgnoreCase(tag)) {
						return eventReader.nextEvent().asCharacters().getData();
					}
				}
			}
		} catch (FileNotFoundException | XMLStreamException e) {
			e.printStackTrace();
		} finally {
			if (eventReader != null) {
				try {
					eventReader.close();
				} catch (XMLStreamException e) {
					logger.error("closing stream", e);
				}
			}
		}
		return "";
	}

	private static void fj(List<Sentence> corpus, StatisticsNew stats) {
		ForkJoinPool pool = new ForkJoinPool();

		if (stats.getFilter().getAl() == AnalysisLevel.STRING_LEVEL) {
			alg.ngram.ForkJoin wc = new alg.ngram.ForkJoin(corpus, stats);
			pool.invoke(wc);
		} else if (stats.getFilter().getAl() == AnalysisLevel.WORD_LEVEL) {
			alg.word.ForkJoin wc = new alg.word.ForkJoin(corpus, stats);
			pool.invoke(wc);
		} else {
			// TODO:
			// alg.inflectedJOS.ForkJoin wc = new alg.inflectedJOS.ForkJoin(corpus, stats);
			// pool.invoke(wc);
		}
	}

	// public static void readXMLGos(String path, Statistics stats) {
	// 	boolean in_word = false;
	// 	String taksonomija = "";
	// 	String lemma = "";
	// 	String msd = "";
	// 	String type = stats.isGosOrthMode() ? "orth" : "norm"; // orth & norm
	//
	// 	List<Word> stavek = new ArrayList<>();
	// 	List<Sentence> corpus = new ArrayList<>();
	// 	String sentenceDelimiter = "seg";
	// 	String taxonomyPrefix = "gos.";
	//
	// 	try {
	// 		XMLInputFactory factory = XMLInputFactory.newInstance();
	// 		XMLEventReader eventReader = factory.createXMLEventReader(new FileInputStream(path));
	//
	// 		while (eventReader.hasNext()) {
	// 			XMLEvent event = eventReader.nextEvent();
	//
	// 			switch (event.getEventType()) {
	// 				case XMLStreamConstants.START_ELEMENT:
	//
	// 					StartElement startElement = event.asStartElement();
	// 					String qName = startElement.getName().getLocalPart();
	//
	// 					// "word" node
	// 					if (qName.equals("w")) {
	// 						in_word = true;
	//
	// 						if (type.equals("norm")) {
	// 							// make sure we're looking at <w lemma...> and not <w type...>
	// 							Iterator var = startElement.getAttributes();
	// 							ArrayList<Object> attributes = new ArrayList<>();
	// 							while (var.hasNext()) {
	// 								attributes.add(var.next());
	// 							}
	//
	// 							if (attributes.contains("msd")) {
	// 								msd = String.valueOf(startElement.getAttributeByName(QName.valueOf("msd")).getValue());
	// 							} else {
	// 								msd = null;
	// 							}
	//
	// 							if (attributes.contains("lemma")) {
	// 								lemma = String.valueOf(startElement.getAttributeByName(QName.valueOf("lemma")).getValue());
	// 							}
	// 						}
	// 					}
	// 					// taxonomy node
	// 					else if (qName.equalsIgnoreCase("catRef")) {
	// 						// there are some term nodes at the beginning that are of no interest to us
	// 						// they differ by not having the attribute "ref", so test will equal null
	// 						Attribute test = startElement.getAttributeByName(QName.valueOf("target"));
	//
	// 						if (test != null) {
	// 							// keep only taxonomy properties
	// 							taksonomija = String.valueOf(test.getValue()).replace(taxonomyPrefix, "");
	// 						}
	// 					} else if (qName.equalsIgnoreCase("div")) {
	// 						type = String.valueOf(startElement.getAttributeByName(QName.valueOf("type")).getValue());
	//
	// 					}
	// 					break;
	//
	// 				case XMLStreamConstants.CHARACTERS:
	// 					Characters characters = event.asCharacters();
	//
	// 					// "word" node value
	// 					if (in_word) {
	// 						if (type.equals("norm") && msd != null) {
	// 							stavek.add(new Word(characters.getData(), lemma, msd));
	// 						} else {
	// 							stavek.add(new Word(characters.getData()));
	// 						}
	//
	// 						in_word = false;
	// 					}
	// 					break;
	//
	// 				case XMLStreamConstants.END_ELEMENT:
	// 					EndElement endElement = event.asEndElement();
	//
	// 					// parser reached end of the current sentence
	// 					if (endElement.getName().getLocalPart().equals(sentenceDelimiter)) {
	// 						// add sentence to corpus
	// 						corpus.add(new Sentence(stavek, taksonomija, type));
	// 						// and start a new one
	// 						stavek = new ArrayList<>();
	//
	// 						/* Invoke Fork-Join when we reach maximum limit of
	// 						 * sentences (because we can't read everything to
	// 						 * memory) or we reach the end of the file.
	// 						 */
	// 						if (corpus.size() == Settings.CORPUS_SENTENCE_LIMIT || !eventReader.hasNext()) {
	// 							fj(corpus, stats);
	// 							// empty the current corpus, since we don't need
	// 							// the data anymore
	// 							corpus.clear();
	// 						}
	// 					}
	//
	// 					// backup
	// 					if (endElement.getName().getLocalPart().equalsIgnoreCase("tei")) {
	// 						fj(corpus, stats);
	// 						corpus.clear();
	// 					}
	//
	// 					break;
	// 			}
	// 		}
	// 	} catch (FileNotFoundException | XMLStreamException e) {
	// 		e.printStackTrace();
	// 	}
	// }

	@SuppressWarnings("unused")
	public static void readXMLSolar(String path, StatisticsNew stats) {
		boolean in_word = false;
		String lemma = "";
		String msd = "";

		List<Word> stavek = new ArrayList<>();
		List<Sentence> corpus = new ArrayList<>();

		// used for filter
		Set<String> headTags = new HashSet<>(Arrays.asList("sola", "predmet", "razred", "regija", "tip", "leto"));
		Map<String, String> headBlock = null;
		boolean includeThisBlock = false;

		try {
			XMLInputFactory factory = XMLInputFactory.newInstance();
			XMLEventReader eventReader = factory.createXMLEventReader(new FileInputStream(path));

			while (eventReader.hasNext()) {
				XMLEvent event = eventReader.nextEvent();

				switch (event.getEventType()) {
					case XMLStreamConstants.START_ELEMENT:

						StartElement startElement = event.asStartElement();
						// System.out.println(String.format("%s", startElement.toString()));
						String qName = startElement.getName().getLocalPart();

						// "word" node
						if (qName.equals("w3")) {
							in_word = true;

							msd = String.valueOf(startElement.getAttributeByName(QName.valueOf("msd")).getValue());
							lemma = String.valueOf(startElement.getAttributeByName(QName.valueOf("lemma")).getValue());
						} else if (qName.equals("c3")) {
							String c3Content = eventReader.nextEvent().asCharacters().getData();

							if (c3Content.equals(".") && includeThisBlock) {
								// add sentence to corpus
								corpus.add(new Sentence(stavek));
								// and start a new one
								stavek = new ArrayList<>();

							/* Invoke Fork-Join when we reach maximum limit of
							 * sentences (because we can't read everything to
							 * memory) or we reach the end of the file.
							 */
								if (corpus.size() == Settings.CORPUS_SENTENCE_LIMIT || !eventReader.hasNext()) {
									fj(corpus, stats);
									// empty the current corpus, since we don't need
									// the data anymore
									corpus.clear();
								}
							}
						} else if (headTags.contains(qName)) {
							String tagContent = eventReader.nextEvent().asCharacters().getData();
							headBlock.put(qName, tagContent);
						} else if (qName.equals("head")) {
							headBlock = new HashMap<>();
						}

						break;

					case XMLStreamConstants.CHARACTERS:
						Characters characters = event.asCharacters();

						// "word" node value
						if (in_word) {
							stavek.add(new Word(characters.getData(), lemma, msd));
							in_word = false;
						}
						break;

					case XMLStreamConstants.END_ELEMENT:
						EndElement endElement = event.asEndElement();
						String qNameEnd = endElement.getName().getLocalPart();

						if (qNameEnd.equals("head")) {
							// validate and set boolean
							if (validateHeadBlock(headBlock, stats.getFilter().getSolarFilters())) {
								includeThisBlock = true;
							}
						} else if (qNameEnd.equals("body")) {
							// new block, reset filter status
							includeThisBlock = false;
						}

						// backup
						if (endElement.getName().getLocalPart().equalsIgnoreCase("korpus")) {
							fj(corpus, stats);
							corpus.clear();
						}

						break;
				}
			}
		} catch (FileNotFoundException | XMLStreamException e) {
			e.printStackTrace();
		}
	}

	/**
	 * @param readHeadBlock block of tags read from the corpus
	 * @param userSetFilter tags with values set by the user
	 *
	 * @return
	 */
	private static boolean validateHeadBlock(Map<String, String> readHeadBlock, HashMap<String, HashSet<String>> userSetFilter) {
		boolean pass = true;

		if (userSetFilter == null) {
			return true;
		}

		for (Map.Entry<String, HashSet<String>> filterEntry : userSetFilter.entrySet()) {
			String key = filterEntry.getKey();
			HashSet<String> valueObject = filterEntry.getValue();

			// if (valueObject instanceof String) {
			// 	pass = validateHeadBlockEntry(readHeadBlock, key, (String) valueObject);
			// } else
			if (valueObject != null) {
				//noinspection unchecked
				for (String value : valueObject) {
					pass = validateHeadBlockEntry(readHeadBlock, key, value);
				}
			}

			if (!pass) {
				// current head block does not include one of the set filters - not likely, but an edge case anyway
				return false;
			}
		}

		// if it gets to this point, it passed all the filters
		return true;
	}

	private static boolean validateHeadBlockEntry(Map<String, String> readHeadBlock, String userSetKey, String userSetValue) {
		if (!readHeadBlock.keySet().contains(userSetKey)) {
			// current head block does not include one of the set filters - not likely, but an edge case anyway
			return false;
		} else if (!readHeadBlock.get(userSetKey).equals(userSetValue)) {
			// different values -> doesn't pass the filter
			return false;
		}

		return true;
	}

	/**
	 * Parses XML headers for information about its taxonomy (if supported) or filters (solar)
	 *
	 * @param filepath
	 * @param corpusIsSplit is corpus split into multiple xml files, or are all entries grouped into one large xml file
	 * @param corpusType
	 */
	public static Object readXmlHeaderTaxonomyAndFilters(String filepath, boolean corpusIsSplit, CorpusType corpusType) {
		boolean parseTaxonomy = Tax.getCorpusTypesWithTaxonomy().contains(corpusType);
		// solar
		Set<String> headTags = null;
		HashMap<String, HashSet<String>> resultFilters = new HashMap<>();
		// taxonomy corpora
		HashSet<String> resultTaxonomy = new HashSet<>();

		String headTagName;

		if (corpusType == CorpusType.SOLAR) {
			headTagName = "head";
			// used for filter
			headTags = new HashSet<>(Arrays.asList(SOLA, PREDMET, RAZRED, REGIJA, TIP, LETO));

			// init results now to avoid null pointers
			headTags.forEach(f -> resultFilters.put(f, new HashSet<>()));
		} else {
			headTagName = "teiHeader";
		}

		XMLInputFactory factory = XMLInputFactory.newInstance();
		XMLEventReader xmlEventReader = null;
		try {
			xmlEventReader = factory.createXMLEventReader(new FileInputStream(filepath));
			boolean insideHeader = false;

			while (xmlEventReader.hasNext()) {
				XMLEvent xmlEvent = xmlEventReader.nextEvent();

				if (xmlEvent.isStartElement()) {
					StartElement startElement = xmlEvent.asStartElement();
					String elementName = startElement.getName().getLocalPart();

					if (elementName.equalsIgnoreCase(headTagName)) {
						// if the corpus is split into files, we skip bodies
						// this toggle is true when we're inside a header (next block of code executes)
						// and false when we're not (skip reading unnecessary attributes)
						insideHeader = true;
					}

					if (insideHeader) {
						if (parseTaxonomy && elementName.equalsIgnoreCase("catRef")) {
							HashMap<String, String> atts = extractAttributes(startElement);
							String debug = "";

							String tax = startElement.getAttributeByName(QName.valueOf("target"))
									.getValue()
									.replace("#", "");

							resultTaxonomy.add(tax);
						} else if (!parseTaxonomy && headTags.contains(elementName)) {
							String tagContent = xmlEventReader.nextEvent().asCharacters().getData();
							resultFilters.get(elementName).add(tagContent);
						}
					}
				} else if (xmlEvent.isEndElement() && corpusIsSplit && isEndElementEndOfHeader(xmlEvent, headTagName)) {
					// if the corpus is split into multiple files, each with only one header block per file
					// that means we should stop after we reach the end of the header
					return parseTaxonomy ? resultTaxonomy : resultFilters;
				} else if (xmlEvent.isEndElement() && !corpusIsSplit && isEndElementEndOfHeader(xmlEvent, headTagName)) {
					// whole corpus in one file, so we have to continue reading in order to find all header blocks
					insideHeader = false;
				}
			}
		} catch (XMLStreamException e) {
			logger.error("Streaming error", e);
			return parseTaxonomy ? resultTaxonomy : resultFilters;
		} catch (FileNotFoundException e) {
			logger.error("File not found", e);
			return parseTaxonomy ? resultTaxonomy : resultFilters;
			// TODO: keep a list of files that threw this error and a dirty boolean marker -> if true, alert user
		} finally {
			if (xmlEventReader != null) {
				try {
					xmlEventReader.close();
				} catch (XMLStreamException e) {
					logger.error("closing stream", e);
				}
			}
		}
		return parseTaxonomy ? resultTaxonomy : resultFilters;
	}

	private static boolean isEndElementEndOfHeader(XMLEvent event, String headerTag) {
		return event.asEndElement()
				.getName()
				.getLocalPart()
				.equalsIgnoreCase(headerTag);
	}

	@SuppressWarnings("Duplicates")
	public static boolean readXMLGigafida(String path, StatisticsNew stats) {
		boolean inWord = false;
		ArrayList<String> currentFiletaxonomy = new ArrayList<>();
		String lemma = "";
		String msd = "";

		List<Word> sentence = new ArrayList<>();
		List<Sentence> corpus = new ArrayList<>(Settings.CORPUS_SENTENCE_LIMIT); // preset the list's size, so there won't be a need to resize it
		String sentenceDelimiter = "s";

		XMLEventReader eventReader = null;
		try {
			XMLInputFactory factory = XMLInputFactory.newInstance();
			eventReader = factory.createXMLEventReader(new FileInputStream(path));

			while (eventReader.hasNext()) {
				XMLEvent event = eventReader.nextEvent();

				switch (event.getEventType()) {
					case XMLStreamConstants.START_ELEMENT:
						StartElement startElement = event.asStartElement();
						String qName = startElement.getName().getLocalPart();

						// "word" node
						if (qName.equals("w")) {
							inWord = true;

							msd = String.valueOf(startElement.getAttributeByName(QName.valueOf("msd")).getValue());
							lemma = String.valueOf(startElement.getAttributeByName(QName.valueOf("lemma")).getValue());
						}
						// taxonomy node
						else if (qName.equalsIgnoreCase("catRef")) {
							// there are some term nodes at the beginning that are of no interest to us
							// they differ by not having the attribute "ref", so test will equal null
							Attribute tax = startElement.getAttributeByName(QName.valueOf("target"));

							if (tax != null) {
								// keep only taxonomy properties
								currentFiletaxonomy.add(String.valueOf(tax.getValue()).replace("#", ""));
							}
						}
						break;

					case XMLStreamConstants.CHARACTERS:
						Characters characters = event.asCharacters();

						// "word" node value
						if (inWord) {
							String word = characters.getData();
							sentence.add(new Word(word, lemma, msd));
							inWord = false;
						}
						break;

					case XMLStreamConstants.END_ELEMENT:
						EndElement endElement = event.asEndElement();

						String var = endElement.getName().getLocalPart();
						String debug = "";

						// parser reached end of the current sentence
						if (endElement.getName().getLocalPart().equals(sentenceDelimiter)) {
							// add sentence to corpus if it passes filters
							sentence = runFilters(sentence, stats.getFilter());

							if (!ValidationUtil.isEmpty(sentence)) {
								corpus.add(new Sentence(sentence));
							}

							// and start a new one
							sentence = new ArrayList<>();

							/* Invoke Fork-Join when we reach maximum limit of
							 * sentences (because we can't read everything to
							 * memory) or we reach the end of the file.
							 */
							if (corpus.size() == Settings.CORPUS_SENTENCE_LIMIT || !eventReader.hasNext()) {
								fj(corpus, stats);
								// empty the current corpus, since we don't need the data anymore
								corpus.clear();

								// TODO: if (stats.isUseDB()) {
								// 	stats.storeTmpResultsToDB();
								// }
							}
						} else if (endElement.getName().getLocalPart().equals("teiHeader")) {
							// before proceeding to read this file, make sure that taxonomy filters are a match

							if (!ValidationUtil.isEmpty(stats.getFilter().getTaxonomy())) {
								currentFiletaxonomy.retainAll(stats.getFilter().getTaxonomy()); // intersection

								if (currentFiletaxonomy.isEmpty()) {
									// taxonomies don't match so stop
									return false;
								}
							}
						}

						// fallback
						else if (endElement.getName().getLocalPart().equalsIgnoreCase("tei")) {
							fj(corpus, stats);
							corpus.clear();

							// TODO: if (stats.isUseDB()) {
							// 	stats.storeTmpResultsToDB();
							// }
						}

						break;
				}
			}
		} catch (FileNotFoundException | XMLStreamException e) {
			e.printStackTrace();
		} finally {
			if (eventReader != null) {
				try {
					eventReader.close();
				} catch (XMLStreamException e) {
					logger.error("closing stream", e);
				}
			}
		}

		return true;
	}

	@SuppressWarnings("Duplicates")
	public static boolean readXMLGos(String path, StatisticsNew stats) {
		boolean inWord = false;
		boolean inOrthDiv = false;
		boolean computeForOrth = stats.getCorpus().isGosOrthMode();
		ArrayList<String> currentFiletaxonomy = new ArrayList<>();
		String lemma = "";
		String msd = "";

		List<Word> sentence = new ArrayList<>();
		List<Sentence> corpus = new ArrayList<>(Settings.CORPUS_SENTENCE_LIMIT); // preset the list's size, so there won't be a need to resize it
		String sentenceDelimiter = "seg";

		String gosType = stats.getFilter().hasMsd() ? "norm" : "orth"; // orth & norm

		XMLEventReader eventReader = null;

		boolean includeFile = true;

		try {
			XMLInputFactory factory = XMLInputFactory.newInstance();
			eventReader = factory.createXMLEventReader(new FileInputStream(path));

			while (eventReader.hasNext()) {
				XMLEvent event = eventReader.nextEvent();
				// System.out.print(String.format("%s", event.toString().replaceAll("\\['http://www.tei-c.org/ns/1.0'\\]::", "")));

				switch (event.getEventType()) {
					case XMLStreamConstants.START_ELEMENT:
						StartElement startElement = event.asStartElement();
						String qName = startElement.getName().getLocalPart();

						if (qName.equals("div")) {
							HashMap<String, String> atts = extractAttributes(startElement);

							if (atts.keySet().contains("type")) {
								inOrthDiv = atts.get("type").equals("orth");
							}
						}

						// "word" node
						if (qName.equals("w")) {
							// check that it's not a type
							HashMap<String, String> atts = extractAttributes(startElement);

							if (!atts.containsKey("type")) {
								inWord = true;

								if (atts.containsKey("msd")) {
									msd = atts.get("msd");

								}
								if (atts.containsKey("lemma")) {
									lemma = atts.get("lemma");
								}
								//
								// if (!inOrthDiv) {
								// 	msd = String.valueOf(startElement.getAttributeByName(QName.valueOf("msd")).getValue());
								// 	lemma = String.valueOf(startElement.getAttributeByName(QName.valueOf("lemma")).getValue());
								// }
							}

							// }
						}
						// taxonomy node
						else if (qName.equalsIgnoreCase("catRef")) {
							// there are some term nodes at the beginning that are of no interest to us
							// they differ by not having the attribute "ref", so test will equal null
							Attribute tax = startElement.getAttributeByName(QName.valueOf("target"));

							if (tax != null) {
								// keep only taxonomy properties
								currentFiletaxonomy.add(String.valueOf(tax.getValue()));
							}
						} else if (qName.equalsIgnoreCase("div")) {
							gosType = String.valueOf(startElement.getAttributeByName(QName.valueOf("type")).getValue());
						}
						break;

					case XMLStreamConstants.CHARACTERS:
						// "word" node value
						if (inWord) {
							Characters characters = event.asCharacters();
							if (gosType.equals("norm") && msd != null) {
								sentence.add(new Word(characters.getData(), lemma, msd));
							} else {
								sentence.add(new Word(characters.getData()));
							}

							inWord = false;
						}
						break;

					case XMLStreamConstants.END_ELEMENT:
						EndElement endElement = event.asEndElement();

						// parser reached end of the current sentence
						if (endElement.getName().getLocalPart().equals(sentenceDelimiter)) {
							// add sentence to corpus if it passes filters
							boolean saveSentence = computeForOrth == inOrthDiv;

							if (includeFile && saveSentence && !ValidationUtil.isEmpty(sentence)) {
								sentence = runFilters(sentence, stats.getFilter());
								corpus.add(new Sentence(sentence));
							}

							// and start a new one
							sentence = new ArrayList<>();

							/* Invoke Fork-Join when we reach maximum limit of
							 * sentences (because we can't read everything to
							 * memory) or we reach the end of the file.
							 */
							if (corpus.size() == Settings.CORPUS_SENTENCE_LIMIT || !eventReader.hasNext()) {
								fj(corpus, stats);
								// empty the current corpus, since we don't need
								// the data anymore
								corpus.clear();
							}
						} else if (endElement.getName().getLocalPart().equals("teiHeader")) {
							// before proceeding to read this file, make sure that taxonomy filters are a match
							if (!ValidationUtil.isEmpty(stats.getFilter().getTaxonomy())) {
								currentFiletaxonomy.retainAll(stats.getFilter().getTaxonomy()); // intersection

								// disregard this entry if taxonomies don't match
								includeFile = !currentFiletaxonomy.isEmpty();

								currentFiletaxonomy = new ArrayList<>();
							}
						}

						// backup
						else if (endElement.getName().getLocalPart().equalsIgnoreCase("tei")) {
							fj(corpus, stats);
							corpus.clear();
						}

						break;
				}
			}
		} catch (FileNotFoundException | XMLStreamException e) {
			e.printStackTrace();
		} finally {
			if (eventReader != null) {
				try {
					eventReader.close();
				} catch (XMLStreamException e) {
					logger.error("closing stream", e);
				} catch (Exception e) {
					logger.error("general error", e);
				}
			}
		}

		return true;
	}

	/**
	 * Runs the sentence through some filters, so we don't do calculations when unnecessary.
	 * Filters:
	 * <ol>
	 * <li><b>Ngrams:</b> omit sentences that are shorter than the ngram value (e.g. 3 gram of a single word sentence)</li>
	 * <li><b>Letter ngrams:</b> omit words that are shorter than the specified string length (e.g. combinations of 3 letters when the word consists of only 2 letters)</li>
	 * </ol>
	 *
	 * @return Empty sentence (if fails 1.) or a sentence with some words removed (2.)
	 */
	private static List<Word> runFilters(List<Word> sentence, Filter filter) {
		if (filter.getAl() == AnalysisLevel.STRING_LEVEL) {
			// ngram level: if not 0 must be less than or equal to number of words in this sentence.
			if (filter.getNgramValue() > 0 && filter.getNgramValue() > sentence.size()) {
				return null;
			}

			// if we're calculating values for letters, omit words that are shorter than string length
			if (filter.getNgramValue() == 0) {
				sentence.removeIf(w -> (filter.getCalculateFor() == CalculateFor.WORD && w.getWord().length() < filter.getStringLength())
						|| (filter.getCalculateFor() == CalculateFor.LEMMA && w.getLemma().length() < filter.getStringLength()));
			}
		}

		return sentence;
	}

	private static HashMap<String, String> extractAttributes(StartElement se) {
		Iterator attributesIt = se.getAttributes();
		HashMap<String, String> atts = new HashMap<>();

		while (attributesIt.hasNext()) {
			Attribute a = (Attribute) attributesIt.next();
			atts.put(a.getName().getLocalPart(), a.getValue());
		}

		return atts;
	}
}