List of usage examples for org.apache.commons.lang.math LongRange getMinimumLong
public long getMinimumLong()
Gets the minimum number in this range as a long.
From source file:SparkKMer.java
public static void main(String[] args) throws Exception { //Setup/*from w w w . java2s. c om*/ SparkConf sparkConf = new SparkConf().setAppName("SparkKMer"); JavaSparkContext jsc = new JavaSparkContext(sparkConf); //Agrument parsing if (args.length < 2) { System.err.println("Usage: SparkKMer <accession> <kmer-length>"); System.exit(1); } final String acc = args[0]; final int KMER_LENGTH = Integer.parseInt(args[1]); //Check accession and split ReadCollection run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc); long numreads = run.getReadCount(); //Slice the job int chunk = 20000; /** amount of reads per 1 map operation **/ int slices = (int) (numreads / chunk / 1); if (slices == 0) slices = 1; List<LongRange> sub = new ArrayList<LongRange>(); for (long first = 1; first <= numreads;) { long last = first + chunk - 1; if (last > numreads) last = numreads; sub.add(new LongRange(first, last)); first = last + 1; } System.err.println("Prepared ranges: \n" + sub); JavaRDD<LongRange> jobs = jsc.parallelize(sub, slices); //Map // JavaRDD<String> kmers = jobs.flatMap(new FlatMapFunction<LongRange, String>() { ReadCollection run = null; @Override public Iterable<String> call(LongRange s) { //Executes on task nodes List<String> ret = new ArrayList<String>(); try { long first = s.getMinimumLong(); long last = s.getMaximumLong(); if (run == null) { run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc); } ReadIterator it = run.getReadRange(first, last - first + 1, Read.all); while (it.nextRead()) { //iterate through fragments while (it.nextFragment()) { String bases = it.getFragmentBases(); //iterate through kmers for (int i = 0; i < bases.length() - KMER_LENGTH; i++) { ret.add(bases.substring(i, i + KMER_LENGTH)); } } } } catch (ErrorMsg x) { System.err.println(x.toString()); x.printStackTrace(); } return ret; } }); //Initiate kmer counting; JavaPairRDD<String, Integer> kmer_ones = kmers.mapToPair(new PairFunction<String, String, Integer>() { @Override public Tuple2<String, Integer> call(String s) { return new Tuple2<String, Integer>(s, 1); } }); //Reduce counts JavaPairRDD<String, Integer> counts = kmer_ones.reduceByKey(new Function2<Integer, Integer, Integer>() { @Override public Integer call(Integer i1, Integer i2) { return i1 + i2; } }); //Collect the output List<Tuple2<String, Integer>> output = counts.collect(); for (Tuple2<String, Integer> tuple : output) { System.out.println(tuple._1() + ": " + tuple._2()); } jsc.stop(); }
From source file:com.hipu.bdb.util.FileUtils.java
public static LongRange expandRange(LongRange range1, LongRange range2) { return new LongRange(Math.min(range1.getMinimumLong(), range2.getMinimumLong()), Math.max(range1.getMaximumLong(), range2.getMaximumLong())); }
From source file:com.hipu.bdb.util.FileUtils.java
/** * Retrieve a number of lines from the file around the given * position, as when paging forward or backward through a file. * /* w w w . java 2 s. c o m*/ * @param file File to retrieve lines * @param position offset to anchor lines * @param signedDesiredLineCount lines requested; if negative, * want this number of lines ending with a line containing * the position; if positive, want this number of lines, * all starting at or after position. * @param lines List<String> to insert found lines * @param lineEstimate int estimate of line size, 0 means use default * of 128 * @return LongRange indicating the file offsets corresponding to * the beginning of the first line returned, and the point * after the end of the last line returned * @throws IOException */ @SuppressWarnings("unchecked") public static LongRange pagedLines(File file, long position, int signedDesiredLineCount, List<String> lines, int lineEstimate) throws IOException { // consider negative positions as from end of file; -1 = last byte if (position < 0) { position = file.length() + position; } // calculate a reasonably sized chunk likely to have all desired lines if (lineEstimate == 0) { lineEstimate = 128; } int desiredLineCount = Math.abs(signedDesiredLineCount); long startPosition; long fileEnd = file.length(); int bufferSize = (desiredLineCount + 5) * lineEstimate; if (signedDesiredLineCount > 0) { // reading forward; include previous char in case line-end startPosition = position - 1; } else { // reading backward startPosition = position - bufferSize + (2 * lineEstimate); } if (startPosition < 0) { startPosition = 0; } if (startPosition + bufferSize > fileEnd) { bufferSize = (int) (fileEnd - startPosition); } // read that reasonable chunk FileInputStream fis = new FileInputStream(file); fis.getChannel().position(startPosition); byte[] buf = new byte[bufferSize]; IOUtils.closeQuietly(fis); // find all line starts fully in buffer // (positions after a line-end, per line-end definition in // BufferedReader.readLine) LinkedList<Integer> lineStarts = new LinkedList<Integer>(); if (startPosition == 0) { lineStarts.add(0); } boolean atLineEnd = false; boolean eatLF = false; int i; for (i = 0; i < bufferSize; i++) { if ((char) buf[i] == '\n' && eatLF) { eatLF = false; continue; } if (atLineEnd) { atLineEnd = false; lineStarts.add(i); if (signedDesiredLineCount < 0 && startPosition + i > position) { // reached next line past position, read no more break; } } if ((char) buf[i] == '\r') { atLineEnd = true; eatLF = true; continue; } if ((char) buf[i] == '\n') { atLineEnd = true; } } if (startPosition + i == fileEnd) { // add phantom lineStart after end lineStarts.add(bufferSize); } int foundFullLines = lineStarts.size() - 1; // if found no lines if (foundFullLines < 1) { if (signedDesiredLineCount > 0) { if (startPosition + bufferSize == fileEnd) { // nothing more to read: return nothing return new LongRange(fileEnd, fileEnd); } else { // retry with larger lineEstimate return pagedLines(file, position, signedDesiredLineCount, lines, Math.max(bufferSize, lineEstimate)); } } else { // try again with much larger line estimate // TODO: fail gracefully before growing to multi-MB buffers return pagedLines(file, position, signedDesiredLineCount, lines, bufferSize); } } // trim unneeded lines while (signedDesiredLineCount > 0 && startPosition + lineStarts.getFirst() < position) { // discard lines starting before desired position lineStarts.removeFirst(); } while (lineStarts.size() > desiredLineCount + 1) { if (signedDesiredLineCount < 0 && (startPosition + lineStarts.get(1) <= position)) { // discard from front until reach line containing target position lineStarts.removeFirst(); } else { lineStarts.removeLast(); } } int firstLine = lineStarts.getFirst(); int partialLine = lineStarts.getLast(); LongRange range = new LongRange(startPosition + firstLine, startPosition + partialLine); List<String> foundLines = IOUtils .readLines(new ByteArrayInputStream(buf, firstLine, partialLine - firstLine)); if (foundFullLines < desiredLineCount && signedDesiredLineCount < 0 && startPosition > 0) { // if needed and reading backward, read more lines from earlier range = expandRange(range, pagedLines(file, range.getMinimumLong() - 1, signedDesiredLineCount + foundFullLines, lines, bufferSize / foundFullLines)); } lines.addAll(foundLines); if (signedDesiredLineCount < 0 && range.getMaximumLong() < position) { // did not get line containining start position range = expandRange(range, pagedLines(file, partialLine, 1, lines, bufferSize / foundFullLines)); } if (signedDesiredLineCount > 0 && foundFullLines < desiredLineCount && range.getMaximumLong() < fileEnd) { // need more forward lines range = expandRange(range, pagedLines(file, range.getMaximumLong(), desiredLineCount - foundFullLines, lines, bufferSize / foundFullLines)); } return range; }
From source file:de.tor.tribes.ui.algo.TimeFrameVisualizer.java
private void updateSize() { LongRange startRange = mTimeFrame.getStartRange(); LongRange arriveRange = mTimeFrame.getArriveRange(); long minValue = startRange.getMinimumLong(); long maxValue = arriveRange.getMaximumLong(); Dimension size = new Dimension(Math.round( (maxValue - minValue + 240 * (int) DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_MINUTE), getHeight());//w ww . j a v a 2 s. c o m if (size.getWidth() < mParent.getWidth()) { size = mParent.getSize(); } setMinimumSize(size); setMaximumSize(size); setPreferredSize(size); mParent.getViewport().setViewSize(size); }
From source file:de.tor.tribes.ui.algo.TimeFrameVisualizer.java
private void renderRange(LongRange pRange, LongRange pStartRange, LongRange pArriveRange, boolean pIsStartRange, boolean pIsArriveRange, Graphics2D pG2D, TimeSpan pSpanForRange, HashMap<String, Object> pPopupInfo) { int rangeStart = 0; int rangeWidth = 0; if (pRange.overlapsRange(pStartRange)) { //start range rendering long startDelta = pStartRange.getMinimumLong(); rangeStart = Math.round((pRange.getMinimumLong() - startDelta) / DateUtils.MILLIS_PER_MINUTE); // int rangeEnd = Math.round((pRange.getMaximumLong() - startDelta) / DateUtils.MILLIS_PER_MINUTE); rangeWidth = Math//from w ww. j a va2 s. c o m .round((pRange.getMaximumLong() - pRange.getMinimumLong()) / DateUtils.MILLIS_PER_MINUTE); } else if (pRange.overlapsRange(pArriveRange)) { //end range rendering long startDelta = pStartRange.getMinimumLong(); rangeStart = Math.round((pRange.getMinimumLong() - startDelta) / DateUtils.MILLIS_PER_MINUTE); // int rangeEnd = Math.round((pRange.getMaximumLong() - arriveDelta) / DateUtils.MILLIS_PER_MINUTE); rangeWidth = Math .round((pRange.getMaximumLong() - pRange.getMinimumLong()) / DateUtils.MILLIS_PER_MINUTE); } //correct small widths if (rangeWidth == 0) { rangeWidth = 5; } long max = Math.round( (pArriveRange.getMaximumLong() - pStartRange.getMinimumLong()) / DateUtils.MILLIS_PER_MINUTE); if (rangeStart > max) { return; } SimpleDateFormat f = new SimpleDateFormat("dd.MM.yy HH:mm:ss"); String labelString = ""; if (pSpanForRange != null) { labelString = pSpanForRange.toString(); } else { labelString = f.format(new Date(pRange.getMinimumLong())) + " bis " + f.format(new Date(pRange.getMaximumLong())); } Rectangle2D labelBounds = pG2D.getFontMetrics().getStringBounds(labelString, pG2D); if (pIsStartRange) { pG2D.setColor(Color.RED); pG2D.fillRect(rangeStart, 20, rangeWidth, 20); pG2D.setColor(Color.BLACK); pG2D.drawRect(rangeStart, 20, rangeWidth, 20); pG2D.setColor(Color.RED); pG2D.setFont(pG2D.getFont().deriveFont(Font.BOLD, 14.0f)); pG2D.drawString(labelString, rangeStart, (int) labelBounds.getHeight()); } else if (pIsArriveRange) { pG2D.setColor(Color.GREEN.darker()); pG2D.fillRect(rangeStart, 20, rangeWidth, 20); pG2D.setColor(Color.BLACK); pG2D.drawRect(rangeStart, 20, rangeWidth, 20); pG2D.setColor(Color.GREEN.darker()); pG2D.setFont(pG2D.getFont().deriveFont(Font.BOLD, 14.0f)); pG2D.drawString(labelString, rangeStart, (int) labelBounds.getHeight() + 40); } else { pG2D.fillRect(rangeStart, 20, rangeWidth, 20); pG2D.setColor(Color.BLACK); pG2D.drawRect(rangeStart, 20, rangeWidth, 20); Point loc = getMousePosition(); if (loc != null && new Rectangle(rangeStart, 20, rangeWidth, 20).contains(loc)) { pPopupInfo.put("popup.location", loc); pPopupInfo.put("popup.label", labelString); pPopupInfo.put("active.range", pRange); pPopupInfo.put("span.for.range", pSpanForRange); } } }
From source file:de.tor.tribes.ui.algo.TimeFrameVisualizer.java
@Override public void paintComponent(Graphics g) { super.paintComponent(g); if (mTimeFrame == null) { renderNoInfoView(g);/* w w w .j a va 2 s.com*/ } else { updateSize(); LongRange startRange = mTimeFrame.getStartRange(); LongRange arriveRange = mTimeFrame.getArriveRange(); HashMap<LongRange, TimeSpan> startRanges = mTimeFrame .startTimespansToRangesMap(AnyTribe.getSingleton()); HashMap<LongRange, TimeSpan> arriveRanges = mTimeFrame.arriveTimespansToRangesMap(null); long minValue = startRange.getMinimumLong(); long maxValue = arriveRange.getMaximumLong(); Graphics2D g2d = (Graphics2D) g; g2d.setPaint(new TexturePaint(STROKED, new Rectangle(0, 0, 3, 3))); g2d.fillRect(0, 0, getWidth(), getHeight()); //draw frame around the entire range renderRange(new LongRange(startRange.getMinimumLong(), arriveRange.getMaximumLong()), startRange, arriveRange, false, false, g2d, null, popupInfo); g2d.setColor(Constants.DS_BACK); popupInfo.clear(); //fill start range renderRange(startRange, startRange, arriveRange, true, false, g2d, null, popupInfo); //fill arrive range renderRange(arriveRange, startRange, arriveRange, false, true, g2d, null, popupInfo); Paint p = g2d.getPaint(); Iterator<LongRange> rangeKeys = startRanges.keySet().iterator(); while (rangeKeys.hasNext()) { LongRange currentRange = rangeKeys.next(); TimeSpan spanForRange = startRanges.get(currentRange); if (spanForRange != null) { if (spanForRange.isValidAtEveryDay()) { g2d.setPaint(new TexturePaint(DAILY_START_FRAME_FILL, new Rectangle(0, 0, 3, 3))); } else if (spanForRange.isValidAtExactTime()) { g2d.setPaint(new TexturePaint(EXACT_START_FRAME_FILL, new Rectangle(0, 0, 3, 3))); } else { g2d.setPaint(new TexturePaint(ONE_DAY_START_FRAME_FILL, new Rectangle(0, 0, 3, 3))); } } renderRange(currentRange, startRange, arriveRange, false, false, g2d, spanForRange, popupInfo); } Composite c = g2d.getComposite(); rangeKeys = arriveRanges.keySet().iterator(); while (rangeKeys.hasNext()) { LongRange currentRange = rangeKeys.next(); g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.7f)); g2d.setPaint(new TexturePaint(ARRIVE_FRAME_FILL, new Rectangle(0, 0, 3, 3))); TimeSpan spanForRange = arriveRanges.get(currentRange); renderRange(currentRange, startRange, arriveRange, false, false, g2d, spanForRange, popupInfo); } g2d.setComposite(c); g2d.setPaint(p); renderDayMarkers(minValue, maxValue, g2d); renderPopup(popupInfo, g2d); } }
From source file:net.sourceforge.subsonic.controller.StreamController.java
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response) throws Exception { TransferStatus status = null;// w ww. j a va 2s .c o m PlaylistInputStream in = null; Player player = playerService.getPlayer(request, response, false, true); User user = securityService.getUserByName(player.getUsername()); try { if (!user.isStreamRole()) { response.sendError(HttpServletResponse.SC_FORBIDDEN, "Streaming is forbidden for user " + user.getUsername()); return null; } // If "playlist" request parameter is set, this is a Podcast request. In that case, create a separate // playlist (in order to support multiple parallel Podcast streams). String playlistName = request.getParameter("playlist"); boolean isPodcast = playlistName != null; if (isPodcast) { Playlist playlist = new Playlist(); playlistService.loadPlaylist(playlist, playlistName); player.setPlaylist(playlist); Util.setContentLength(response, playlist.length()); LOG.info("Incoming Podcast request for playlist " + playlistName); } String contentType = StringUtil.getMimeType(request.getParameter("suffix")); response.setContentType(contentType); String preferredTargetFormat = request.getParameter("format"); Integer maxBitRate = ServletRequestUtils.getIntParameter(request, "maxBitRate"); if (Integer.valueOf(0).equals(maxBitRate)) { maxBitRate = null; } VideoTranscodingSettings videoTranscodingSettings = null; // Is this a request for a single file (typically from the embedded Flash player)? // In that case, create a separate playlist (in order to support multiple parallel streams). // Also, enable partial download (HTTP byte range). MediaFile file = getSingleFile(request); boolean isSingleFile = file != null; LongRange range = null; if (isSingleFile) { Playlist playlist = new Playlist(); playlist.addFiles(true, file); player.setPlaylist(playlist); if (!file.isVideo()) { response.setIntHeader("ETag", file.getId()); response.setHeader("Accept-Ranges", "bytes"); } TranscodingService.Parameters parameters = transcodingService.getParameters(file, player, maxBitRate, preferredTargetFormat, videoTranscodingSettings); long fileLength = getFileLength(parameters); boolean isConversion = parameters.isDownsample() || parameters.isTranscode(); boolean estimateContentLength = ServletRequestUtils.getBooleanParameter(request, "estimateContentLength", false); range = getRange(request, file); if (range != null) { LOG.info("Got range: " + range); response.setStatus(HttpServletResponse.SC_PARTIAL_CONTENT); Util.setContentLength(response, fileLength - range.getMinimumLong()); long firstBytePos = range.getMinimumLong(); long lastBytePos = fileLength - 1; response.setHeader("Content-Range", "bytes " + firstBytePos + "-" + lastBytePos + "/" + fileLength); } else if (!isConversion || estimateContentLength) { Util.setContentLength(response, fileLength); } String transcodedSuffix = transcodingService.getSuffix(player, file, preferredTargetFormat); response.setContentType(StringUtil.getMimeType(transcodedSuffix)); if (file.isVideo()) { videoTranscodingSettings = createVideoTranscodingSettings(file, request); } } if (request.getMethod().equals("HEAD")) { return null; } // Terminate any other streams to this player. if (!isPodcast && !isSingleFile) { for (TransferStatus streamStatus : statusService.getStreamStatusesForPlayer(player)) { if (streamStatus.isActive()) { streamStatus.terminate(); } } } status = statusService.createStreamStatus(player); in = new PlaylistInputStream(player, status, maxBitRate, preferredTargetFormat, videoTranscodingSettings, transcodingService, audioScrobblerService, mediaFileService, searchService); OutputStream out = RangeOutputStream.wrap(response.getOutputStream(), range); // Enabled SHOUTcast, if requested. boolean isShoutCastRequested = "1".equals(request.getHeader("icy-metadata")); if (isShoutCastRequested && !isSingleFile) { response.setHeader("icy-metaint", "" + ShoutCastOutputStream.META_DATA_INTERVAL); response.setHeader("icy-notice1", "This stream is served using Subsonic"); response.setHeader("icy-notice2", "Subsonic - Free media streamer - subsonic.org"); response.setHeader("icy-name", "Subsonic"); response.setHeader("icy-genre", "Mixed"); response.setHeader("icy-url", "http://subsonic.org/"); out = new ShoutCastOutputStream(out, player.getPlaylist(), settingsService); } final int BUFFER_SIZE = 2048; byte[] buf = new byte[BUFFER_SIZE]; while (true) { // Check if stream has been terminated. if (status.terminated()) { return null; } if (player.getPlaylist().getStatus() == Playlist.Status.STOPPED) { if (isPodcast || isSingleFile) { break; } else { sendDummy(buf, out); } } else { int n = in.read(buf); if (n == -1) { if (isPodcast || isSingleFile) { break; } else { sendDummy(buf, out); } } else { out.write(buf, 0, n); } } } } finally { if (status != null) { securityService.updateUserByteCounts(user, status.getBytesTransfered(), 0L, 0L); statusService.removeStreamStatus(status); } IOUtils.closeQuietly(in); } return null; }
From source file:net.sourceforge.subsonic.util.StringUtilTestCase.java
License:asdf
private void doTestParseRange(long expectedFrom, long expectedTo, String range) { LongRange actual = StringUtil.parseRange(range); assertEquals("Error in parseRange().", expectedFrom, actual.getMinimumLong()); assertEquals("Error in parseRange().", expectedTo, actual.getMaximumLong()); }
From source file:org.apache.hadoop.yarn.api.protocolrecords.GetApplicationsRequest.java
/** * <p>/*from ww w. j a v a2 s. c o m*/ * The request from clients to get a report of Applications matching the * giving application types in the cluster from the * <code>ResourceManager</code>. * </p> * * @see ApplicationClientProtocol#getApplications(GetApplicationsRequest) * * <p>Setting any of the parameters to null, would just disable that * filter</p> * * @param scope {@link ApplicationsRequestScope} to filter by * @param users list of users to filter by * @param queues list of scheduler queues to filter by * @param applicationTypes types of applications * @param applicationTags application tags to filter by * @param applicationStates application states to filter by * @param startRange range of application start times to filter by * @param finishRange range of application finish times to filter by * @param limit number of applications to limit to * @return {@link GetApplicationsRequest} to be used with * {@link ApplicationClientProtocol#getApplications(GetApplicationsRequest)} */ @Public @Stable public static GetApplicationsRequest newInstance(ApplicationsRequestScope scope, Set<String> users, Set<String> queues, Set<String> applicationTypes, Set<String> applicationTags, EnumSet<YarnApplicationState> applicationStates, LongRange startRange, LongRange finishRange, Long limit) { GetApplicationsRequest request = Records.newRecord(GetApplicationsRequest.class); if (scope != null) { request.setScope(scope); } request.setUsers(users); request.setQueues(queues); request.setApplicationTypes(applicationTypes); request.setApplicationTags(applicationTags); request.setApplicationStates(applicationStates); if (startRange != null) { request.setStartRange(startRange.getMinimumLong(), startRange.getMaximumLong()); } if (finishRange != null) { request.setFinishRange(finishRange.getMinimumLong(), finishRange.getMaximumLong()); } if (limit != null) { request.setLimit(limit); } return request; }
From source file:org.archive.util.FileUtils.java
/** * Retrieve a number of lines from the file around the given * position, as when paging forward or backward through a file. * //from www .j a v a 2 s . c o m * @param file File to retrieve lines * @param position offset to anchor lines * @param signedDesiredLineCount lines requested; if negative, * want this number of lines ending with a line containing * the position; if positive, want this number of lines, * all starting at or after position. * @param lines List<String> to insert found lines * @param lineEstimate int estimate of line size, 0 means use default * of 128 * @return LongRange indicating the file offsets corresponding to * the beginning of the first line returned, and the point * after the end of the last line returned * @throws IOException */ @SuppressWarnings("unchecked") public static LongRange pagedLines(File file, long position, int signedDesiredLineCount, List<String> lines, int lineEstimate) throws IOException { // consider negative positions as from end of file; -1 = last byte if (position < 0) { position = file.length() + position; } // calculate a reasonably sized chunk likely to have all desired lines if (lineEstimate == 0) { lineEstimate = 128; } int desiredLineCount = Math.abs(signedDesiredLineCount); long startPosition; long fileEnd = file.length(); int bufferSize = (desiredLineCount + 5) * lineEstimate; if (signedDesiredLineCount > 0) { // reading forward; include previous char in case line-end startPosition = position - 1; } else { // reading backward startPosition = position - bufferSize + (2 * lineEstimate); } if (startPosition < 0) { startPosition = 0; } if (startPosition + bufferSize > fileEnd) { bufferSize = (int) (fileEnd - startPosition); } // read that reasonable chunk FileInputStream fis = new FileInputStream(file); fis.getChannel().position(startPosition); byte[] buf = new byte[bufferSize]; ArchiveUtils.readFully(fis, buf); IOUtils.closeQuietly(fis); // find all line starts fully in buffer // (positions after a line-end, per line-end definition in // BufferedReader.readLine) LinkedList<Integer> lineStarts = new LinkedList<Integer>(); if (startPosition == 0) { lineStarts.add(0); } boolean atLineEnd = false; boolean eatLF = false; int i; for (i = 0; i < bufferSize; i++) { if ((char) buf[i] == '\n' && eatLF) { eatLF = false; continue; } if (atLineEnd) { atLineEnd = false; lineStarts.add(i); if (signedDesiredLineCount < 0 && startPosition + i > position) { // reached next line past position, read no more break; } } if ((char) buf[i] == '\r') { atLineEnd = true; eatLF = true; continue; } if ((char) buf[i] == '\n') { atLineEnd = true; } } if (startPosition + i == fileEnd) { // add phantom lineStart after end lineStarts.add(bufferSize); } int foundFullLines = lineStarts.size() - 1; // if found no lines if (foundFullLines < 1) { if (signedDesiredLineCount > 0) { if (startPosition + bufferSize == fileEnd) { // nothing more to read: return nothing return new LongRange(fileEnd, fileEnd); } else { // retry with larger lineEstimate return pagedLines(file, position, signedDesiredLineCount, lines, Math.max(bufferSize, lineEstimate)); } } else { // try again with much larger line estimate // TODO: fail gracefully before growing to multi-MB buffers return pagedLines(file, position, signedDesiredLineCount, lines, bufferSize); } } // trim unneeded lines while (signedDesiredLineCount > 0 && startPosition + lineStarts.getFirst() < position) { // discard lines starting before desired position lineStarts.removeFirst(); } while (lineStarts.size() > desiredLineCount + 1) { if (signedDesiredLineCount < 0 && (startPosition + lineStarts.get(1) <= position)) { // discard from front until reach line containing target position lineStarts.removeFirst(); } else { lineStarts.removeLast(); } } int firstLine = lineStarts.getFirst(); int partialLine = lineStarts.getLast(); LongRange range = new LongRange(startPosition + firstLine, startPosition + partialLine); List<String> foundLines = IOUtils .readLines(new ByteArrayInputStream(buf, firstLine, partialLine - firstLine)); if (foundFullLines < desiredLineCount && signedDesiredLineCount < 0 && startPosition > 0) { // if needed and reading backward, read more lines from earlier range = expandRange(range, pagedLines(file, range.getMinimumLong() - 1, signedDesiredLineCount + foundFullLines, lines, bufferSize / foundFullLines)); } lines.addAll(foundLines); if (signedDesiredLineCount < 0 && range.getMaximumLong() < position) { // did not get line containining start position range = expandRange(range, pagedLines(file, partialLine, 1, lines, bufferSize / foundFullLines)); } if (signedDesiredLineCount > 0 && foundFullLines < desiredLineCount && range.getMaximumLong() < fileEnd) { // need more forward lines range = expandRange(range, pagedLines(file, range.getMaximumLong(), desiredLineCount - foundFullLines, lines, bufferSize / foundFullLines)); } return range; }