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protected static String getAttribute(Node node, String name, boolean required) { NamedNodeMap attributes = node.getAttributes(); Node idNode = attributes.getNamedItem(name); if (idNode == null) { if (required) { throw new IllegalArgumentException(toPath(node) + "...
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protected static Iterable<Node> evaluate(Node element, XPathExpression expression, boolean detatch) throws XPathExpressionException { final NodeList nodeList = (NodeList) expression.evaluate(element, XPathConstants.NODESET); return new Iterable<Node>() { @Override ...
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public String getProperty(String key, String defaultValue) { String value = resolver.get(key); return (value == null) ? defaultValue : value; }
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public static ConfigurationOption newConfiguration(String pid) { return new org.ops4j.pax.exam.cm.internal.ConfigurationProvisionOption(pid, new HashMap<String, Object>()); }
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public static ConfigurationOption overrideConfiguration(String pid) { return new org.ops4j.pax.exam.cm.internal.ConfigurationProvisionOption(pid, new HashMap<String, Object>()).override(true) .create(false); }
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public static ConfigurationOption factoryConfiguration(String pid) { return new org.ops4j.pax.exam.cm.internal.ConfigurationProvisionOption(pid, new HashMap<String, Object>()).factory(true); }
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public static Option configurationFolder(File folder, String extension) { if (!folder.exists()) { throw new TestContainerException("folder " + folder + " does not exits"); } List<Option> options = new ArrayList<Option>(); File[] files = folder.listFiles(); for (File ...
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private BundleContext getBundleContext(Bundle bundle, long timeout) { long endTime = System.currentTimeMillis() + timeout; BundleContext bc = null; while (bc == null) { bc = bundle.getBundleContext(); if (bc == null) { if (System.currentTimeMillis() >= end...
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@Produces @RequestScoped public EntityManager getEntityManager(EntityManagerFactory emf) { log.debug("producing EntityManager"); return emf.createEntityManager(); }
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public TestProbeBuilder createProbeBuilder(Object testClassInstance) throws IOException, ExamConfigurationException { if (defaultProbeBuilder == null) { defaultProbeBuilder = system.createProbe(); } TestProbeBuilder probeBuilder = overwriteWithUserDefinition(currentTestClass,...
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public static void streamCopy(final InputStream in, final FileChannel out, final ProgressBar progressBar) throws IOException { NullArgumentException.validateNotNull(in, "Input stream"); NullArgumentException.validateNotNull(out, "Output stream"); final long start = System.currentTimeMill...
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public static void streamCopy(final URL url, final FileChannel out, final ProgressBar progressBar) throws IOException { NullArgumentException.validateNotNull(url, "URL"); InputStream is = null; try { is = url.openStream(); streamCopy(is, out, progressBar); ...
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public void close() throws IOException { if (jarOutputStream != null) { jarOutputStream.close(); } else if (os != null) { os.close(); } }
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private void addDirectory(File root, File directory, String targetPath, ZipOutputStream zos) throws IOException { String prefix = targetPath; if (!prefix.isEmpty() && !prefix.endsWith("/")) { prefix += "/"; } // directory entries are required, or else bundle classpath may be ...
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private void addFile(File root, File file, String prefix, ZipOutputStream zos) throws IOException { FileInputStream fis = new FileInputStream(file); ZipEntry jarEntry = new ZipEntry(prefix + normalizePath(root, file)); zos.putNextEntry(jarEntry); StreamUtils.copyStream(fis, zos, false); ...
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private String normalizePath(File root, File file) { String relativePath = file.getPath().substring(root.getPath().length() + 1); String path = relativePath.replaceAll("\\" + File.separator, "/"); return path; }
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public void copyBootClasspathLibraries() throws IOException { BootClasspathLibraryOption[] bootClasspathLibraryOptions = subsystem .getOptions(BootClasspathLibraryOption.class); for (BootClasspathLibraryOption bootClasspathLibraryOption : bootClasspathLibraryOptions) { UrlReferen...
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public void copyReferencedArtifactsToDeployFolder() { File deploy = new File(karafBase, "deploy"); String[] fileEndings = new String[] { "jar", "war", "zip", "kar", "xml" }; ProvisionOption<?>[] options = subsystem.getOptions(ProvisionOption.class); for (ProvisionOption<?> option : optio...
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public KarafFeaturesOption getDependenciesFeature() { if (subsystem == null) { return null; } try { File featuresXmlFile = new File(karafBase, "test-dependencies.xml"); Writer wr = new OutputStreamWriter(new FileOutputStream(featuresXmlFile), "UTF-8"); ...
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static void writeDependenciesFeature(Writer writer, ProvisionOption<?>... provisionOptions) { XMLOutputFactory xof = XMLOutputFactory.newInstance(); xof.setProperty("javax.xml.stream.isRepairingNamespaces", true); XMLStreamWriter sw = null; try { sw = xof.createXMLStreamWrit...
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public static void extract(URL sourceURL, File targetFolder) throws IOException { if (sourceURL.getProtocol().equals("file")) { if (sourceURL.getFile().indexOf(".zip") > 0) { extractZipDistribution(sourceURL, targetFolder); } else if (sourceURL.getFile...
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public CommandLineBuilder append(final String[] segments) { if (segments != null && segments.length > 0) { final String[] command = new String[commandLine.length + segments.length]; System.arraycopy(commandLine, 0, command, 0, commandLine.length); System.arraycopy(segments, 0...
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public CommandLineBuilder append(final String segment) { if (segment != null && !segment.isEmpty()) { return append(new String[]{segment}); } return this; }
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public static String getArtifactVersion(final String groupId, final String artifactId) { final Properties dependencies = new Properties(); InputStream depInputStream = null; try { String depFilePath = "META-INF/maven/dependencies.properties"; URL fileURL = MavenUtils.clas...
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public static MavenArtifactUrlReference.VersionResolver asInProject() { return new MavenArtifactUrlReference.VersionResolver() { @Override public String getVersion(final String groupId, final String artifactId) { return getArtifactVersion(groupId, artifactId); ...
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public URI buildWar() { if (option.getName() == null) { option.name(UUID.randomUUID().toString()); } processClassPath(); try { File webResourceDir = getWebResourceDir(); File probeWar = new File(tempDir, option.getName() + ".war"); ZipBuild...
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private static void daxpy(double constant, double vector1[], double vector2[]) { if (constant == 0) return; assert vector1.length == vector2.length; for (int i = 0; i < vector1.length; i++) { vector2[i] += constant * vector1[i]; } }
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private static double dot(double vector1[], double vector2[]) { double product = 0; assert vector1.length == vector2.length; for (int i = 0; i < vector1.length; i++) { product += vector1[i] * vector2[i]; } return product; }
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private static double euclideanNorm(double vector[]) { int n = vector.length; if (n < 1) { return 0; } if (n == 1) { return Math.abs(vector[0]); } // this algorithm is (often) more accurate than just summing up the squares and taking the square...
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private static void scale(double constant, double vector[]) { if (constant == 1.0) return; for (int i = 0; i < vector.length; i++) { vector[i] *= constant; } }
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@SuppressWarnings("unused") // Public API public void setAutoScaleEnabled(boolean isAutoScaleEnabled) { this.isAutoScaleEnabled = isAutoScaleEnabled; for (int i = 0, size = foldableItemsMap.size(); i < size; i++) { foldableItemsMap.valueAt(i).setAutoScaleEnabled(isAutoScaleEnabled); ...
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public void setFoldRotation(float rotation) { foldRotation = rotation; topPart.applyFoldRotation(rotation); bottomPart.applyFoldRotation(rotation); setInTransformation(rotation != 0f); scaleFactor = 1f; if (isAutoScaleEnabled && width > 0) { double sin = M...
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public void setRollingDistance(float distance) { final float scaleY = scale * scaleFactor * scaleFactorY; topPart.applyRollingDistance(distance, scaleY); bottomPart.applyRollingDistance(distance, scaleY); }
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public void unfold(View coverView, View detailsView) { if (this.coverView == coverView && this.detailsView == detailsView) { scrollToPosition(1); // Starting unfold animation return; } if ((this.coverView != null && this.coverView != coverView) || (this.d...
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public BytesWritable evaluate(BytesWritable geomref) { if (geomref == null || geomref.getLength() == 0){ LogUtils.Log_ArgumentsNull(LOG); return null; } OGCGeometry ogcGeometry = GeometryUtils.geometryFromEsriShape(geomref); if (ogcGeometry == null){ LogUtils.Log_ArgumentsNull(LOG); return null; ...
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public long getId(double x, double y) { double down = (extentMax - y) / binSize; double over = (x - extentMin) / binSize; return ((long)down * numCols) + (long)over; }
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public void queryEnvelope(long binId, Envelope envelope) { long down = binId / numCols; long over = binId % numCols; double xmin = extentMin + (over * binSize); double xmax = xmin + binSize; double ymax = extentMax - (down * binSize); double ymin = ymax - binSize; envelope.setCoords(xmin, y...
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public void queryEnvelope(double x, double y, Envelope envelope) { double down = (extentMax - y) / binSize; double over = (x - extentMin) / binSize; double xmin = extentMin + (over * binSize); double xmax = xmin + binSize; double ymax = extentMax - (down * binSize); double ymin = ymax - binSize; ...
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@Override public boolean next(LongWritable key, Text value) throws IOException { JsonToken token; // first call to nextKeyValue() so we need to create the parser and move to the // feature array if (parser == null) { parser = new JsonFactory().createJsonParser(inputStream); parser.setCodec(new Obj...
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public static void Log_SRIDMismatch(Log logger, BytesWritable geomref1, BytesWritable geomref2){ logger.error(String.format(messages[MSG_SRID_MISMATCH], GeometryUtils.getWKID(geomref1), GeometryUtils.getWKID(geomref2))); }
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public static int getWKID(BytesWritable geomref){ ByteBuffer bb = ByteBuffer.wrap(geomref.getBytes()); return bb.getInt(0); }
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protected boolean moveToRecordStart() throws IOException { int next = 0; long resetPosition = readerPosition; // The case of split point exactly at whitespace between records, is // handled by forcing it to the split following, in the interest of // better balancing the splits, by consuming the whitespace in...
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@Override public float getProgress() throws IOException { if (reachedEnd) return 1; else { final long filePos = in.position(); final long fileEnd = virtualEnd >>> 16; // Add 1 to the denominator to make sure it doesn't reach 1 here when // filePos == fileEnd. return (float)(filePos - fileStart) / ...
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private int guessNextBGZFPos(int p, int end) throws IOException { for (;;) { for (;;) { in.seek(p); in.read(buf.array(), 0, 4); int n = buf.getInt(0); if (n == BGZF_MAGIC) break; // Skip ahead a bit more than 1 byte if you can. if (n >>> 8 == BGZF_MAGIC << 8 >>> 8) ++p; e...
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private static void writeTerminatorBlock(final OutputStream out, final SAMFormat samOutputFormat) throws IOException { if (SAMFormat.CRAM == samOutputFormat) { CramIO.issueEOF(CramVersions.DEFAULT_CRAM_VERSION, out); // terminate with CRAM EOF container } else if (SAMFormat.BAM == samOutputFormat) { ...
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public static <T extends Locatable> void setIntervals(Configuration conf, List<T> intervals) { setTraversalParameters(conf, intervals, false); }
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public static void unsetTraversalParameters(Configuration conf) { conf.unset(BOUNDED_TRAVERSAL_PROPERTY); conf.unset(INTERVALS_PROPERTY); conf.unset(TRAVERSE_UNPLACED_UNMAPPED_PROPERTY); }
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static QueryInterval[] prepareQueryIntervals( final List<Interval> rawIntervals, final SAMSequenceDictionary sequenceDictionary ) { if ( rawIntervals == null || rawIntervals.isEmpty() ) { return null; } // Convert each SimpleInterval to a QueryInterval final QueryInterval[] convertedIntervals = rawIn...
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private static QueryInterval convertSimpleIntervalToQueryInterval( final Interval interval, final SAMSequenceDictionary sequenceDictionary ) { if (interval == null) { throw new IllegalArgumentException("interval may not be null"); } if (sequenceDictionary == null) { throw new IllegalArgumentException("seque...
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public static void convertQuality(Text quality, BaseQualityEncoding current, BaseQualityEncoding target) { if (current == target) throw new IllegalArgumentException("current and target quality encodinds are the same (" + current + ")"); byte[] bytes = quality.getBytes(); final int len = quality.getLength(); ...
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public static int verifyQuality(Text quality, BaseQualityEncoding encoding) { // set allowed quality range int max, min; if (encoding == BaseQualityEncoding.Illumina) { max = FormatConstants.ILLUMINA_OFFSET + FormatConstants.ILLUMINA_MAX; min = FormatConstants.ILLUMINA_OFFSET; } else if (encoding ==...
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public static void main(String[] args) { if (args.length == 0) { System.out.println( "Usage: BGZFBlockIndex [BGZF block indices...]\n\n"+ "Writes a few statistics about each BGZF block index."); return; } for (String arg : args) { final File f = new File(arg); if (f.isFile() && f.canRead()) ...
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private void init( final Path output, final SAMFileHeader header, final boolean writeHeader, final TaskAttemptContext ctx) throws IOException { init( output.getFileSystem(ctx.getConfiguration()).create(output), header, writeHeader, ctx); ...
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static List<Path> getFilesMatching(Path directory, String syntaxAndPattern, String excludesExt) throws IOException { PathMatcher matcher = directory.getFileSystem().getPathMatcher(syntaxAndPattern); List<Path> parts = Files.walk(directory) .filter(matcher::matches) .filter(path -> excludes...
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static void mergeInto(List<Path> parts, OutputStream out) throws IOException { for (final Path part : parts) { Files.copy(part, out); Files.delete(part); } }
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@Override public List<InputSplit> getSplits(JobContext job) throws IOException { final List<InputSplit> splits = super.getSplits(job); // Align the splits so that they don't cross blocks // addIndexedSplits() requires the given splits to be sorted by file // path, so do so. Although FileInputFormat.getSpli...
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public static WrapSeekable<FSDataInputStream> openPath( FileSystem fs, Path p) throws IOException { return new WrapSeekable<FSDataInputStream>( fs.open(p), fs.getFileStatus(p).getLen(), p); }
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public static SAMFileHeader readSAMHeaderFrom( final InputStream in, final Configuration conf) { final ValidationStringency stringency = getValidationStringency(conf); SamReaderFactory readerFactory = SamReaderFactory.makeDefault() .setOption(SamReaderFactory.Option.EAGERLY_DECODE, false) .setUseAsync...
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public long skip(long n) throws IOException { boolean end = false; long toskip = n; while (toskip > 0 && !end) { if (bufferPosn < bufferLength) { int skipped = (int)Math.min(bufferLength - bufferPosn, toskip); bufferPosn += skipped; toskip -= skipped; } if (bufferPosn >= bufferLength) ...
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@Override public float getProgress() { if (length == 0) return 1; if (!isBGZF) return (float)(in.getPosition() - fileStart) / length; try { if (in.peek() == -1) return 1; } catch (IOException e) { return 1; } // Add 1 to the denominator to make sure that we never report 1 here. return (...
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public void processAlignment(final SAMRecord rec) throws IOException { // write an offset for the first record and for the g-th record thereafter (where // g is the granularity), to be consistent with the index method if (count == 0 || (count + 1) % granularity == 0) { SAMFileSource fileSource = rec.getFileSou...
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public void writeVirtualOffset(long virtualOffset) throws IOException { lb.put(0, virtualOffset); out.write(byteBuffer.array()); }
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public static void index( final InputStream rawIn, final OutputStream out, final long inputSize, final int granularity) throws IOException { final BlockCompressedInputStream in = new BlockCompressedInputStream(rawIn); final ByteBuffer byteBuffer = ByteBuffer.allocate(8); // Enough to fit a long final...
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public static List<Interval> getIntervals(final Configuration conf, final String intervalPropertyName) { final String intervalsProperty = conf.get(intervalPropertyName); if (intervalsProperty == null) { return null; } if (intervalsProperty.isEmpty()) { return Immu...
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@Override public long getLength() { final long vsHi = vStart & ~0xffff; final long veHi = vEnd & ~0xffff; final long hiDiff = veHi - vsHi; return hiDiff == 0 ? ((vEnd & 0xffff) - (vStart & 0xffff)) : hiDiff; }
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private void fixBCFSplits( List<FileSplit> splits, List<InputSplit> newSplits) throws IOException { // addGuessedSplits() requires the given splits to be sorted by file // path, so do so. Although FileInputFormat.getSplits() does, at the time // of writing this, generate them in that order, we shouldn't rel...
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public static boolean parseBoolean(String value, boolean defaultValue) { if (value == null) return defaultValue; value = value.trim(); // any of the following will final String[] acceptedTrue = new String[]{ "yes", "true", "t", "y", "1" }; final String[] acceptedFalse = new String[]{ "no", "false", "f"...
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public static void main(String[] args) { if (args.length == 0) { System.out.println( "Usage: SplittingBAMIndex [splitting BAM indices...]\n\n"+ "Writes a few statistics about each splitting BAM index."); return; } for (String arg : args) { final File f = new File(arg); if (f.isFile() && f.ca...
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public static synchronized void cancelNetworkCall(String url, String requestMethod, long endTime, String exception) { if (url != null) { String id = sanitiseURL(url); if ((connections != null) && (connections.containsKey(id))) { connections.remove(id); } } }
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private static int postRUM(String apiKey, String jsonPayload) { try { if (validateApiKey(apiKey)) { String endpoint = RaygunSettings.getRUMEndpoint(); MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8"); OkHttpClient client = new OkHttpClient.Builder() ...
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public static void init(Context context) { String apiKey = readApiKey(context); init(context, apiKey); }
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public static void init(Context context, String apiKey) { RaygunClient.apiKey = apiKey; RaygunClient.context = context; RaygunClient.appContextIdentifier = UUID.randomUUID().toString(); RaygunLogger.d("Configuring Raygun (v"+RaygunSettings.RAYGUN_CLIENT_VERSION+")"); try { RaygunClient.versi...
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public static void init(Context context, String apiKey, String version) { init(context, apiKey); RaygunClient.version = version; }
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public static void send(Throwable throwable, List tags, Map userCustomData) { RaygunMessage msg = buildMessage(throwable); if (msg == null) { RaygunLogger.e("Failed to send RaygunMessage - due to invalid message being built"); return; } msg.getDetails().setTags(RaygunUtils.mergeLists(Raygu...
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public static void sendPulseTimingEvent(RaygunPulseEventType eventType, String name, long milliseconds) { if (RaygunClient.sessionId == null) { sendPulseEvent(RaygunSettings.RUM_EVENT_SESSION_START); } if (eventType == RaygunPulseEventType.ACTIVITY_LOADED) { if (RaygunClient.shouldIgnoreView(na...
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public static <T extends Tag, V> void register(Class<T> tag, Class<V> type, TagConverter<T, V> converter) throws ConverterRegisterException { if(tagToConverter.containsKey(tag)) { throw new ConverterRegisterException("Type conversion to tag " + tag.getName() + " is already registered."); } ...
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public static <T extends Tag, V> void unregister(Class<T> tag, Class<V> type) { tagToConverter.remove(tag); typeToConverter.remove(type); }
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public static <T extends Tag, V> V convertToValue(T tag) throws ConversionException { if(tag == null || tag.getValue() == null) { return null; } if(!tagToConverter.containsKey(tag.getClass())) { throw new ConversionException("Tag type " + tag.getClass().getName() + " has...
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public static <V, T extends Tag> T convertToTag(String name, V value) throws ConversionException { if(value == null) { return null; } TagConverter<T, V> converter = (TagConverter<T, V>) typeToConverter.get(value.getClass()); if(converter == null) { for(Class<?> c...
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public static void writeTag(OutputStream out, Tag tag) throws IOException { writeTag(out, tag, false); }
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public void setValue(List<Tag> value) throws IllegalArgumentException { this.type = null; this.value.clear(); for(Tag tag : value) { this.add(tag); } }
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public boolean add(Tag tag) throws IllegalArgumentException { if(tag == null) { return false; } // If empty list, use this as tag type. if(this.type == null) { this.type = tag.getClass(); } else if(tag.getClass() != this.type) { throw new Ille...
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public void setValue(Map<String, Tag> value) { this.value = new LinkedHashMap<String, Tag>(value); }
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public <T extends Tag> T get(String tagName) { return (T) this.value.get(tagName); }
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public <T extends Tag> T put(T tag) { return (T) this.value.put(tag.getName(), tag); }
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public <T extends Tag> T remove(String tagName) { return (T) this.value.remove(tagName); }
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public static void register(int id, Class<? extends Tag> tag) throws TagRegisterException { if(idToTag.containsKey(id)) { throw new TagRegisterException("Tag ID \"" + id + "\" is already in use."); } if(tagToId.containsKey(tag)) { throw new TagRegisterException("Tag \"" ...
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public static Class<? extends Tag> getClassFor(int id) { if(!idToTag.containsKey(id)) { return null; } return idToTag.get(id); }
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public static int getIdFor(Class<? extends Tag> clazz) { if(!tagToId.containsKey(clazz)) { return -1; } return tagToId.get(clazz); }
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public static Tag createInstance(int id, String tagName) throws TagCreateException { Class<? extends Tag> clazz = idToTag.get(id); if(clazz == null) { throw new TagCreateException("Could not find tag with ID \"" + id + "\"."); } try { Constructor<? extends Tag> c...
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@Override protected synchronized void onMeasure(int widthMeasureSpec, int heightMeasureSpec) { int width = 200; if (MeasureSpec.UNSPECIFIED != MeasureSpec.getMode(widthMeasureSpec)) { width = MeasureSpec.getSize(widthMeasureSpec); } int height = thumbImage.getHeight() ...
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private void drawThumb(float screenCoord, boolean pressed, Canvas canvas, boolean areSelectedValuesDefault) { Bitmap buttonToDraw; if (!activateOnDefaultValues && areSelectedValuesDefault) { buttonToDraw = thumbDisabledImage; } else { buttonToDraw = pressed ? thumbPressed...
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private void drawThumbShadow(float screenCoord, Canvas canvas) { thumbShadowMatrix.setTranslate(screenCoord + thumbShadowXOffset, textOffset + thumbHalfHeight + thumbShadowYOffset); translatedThumbShadowPath.set(thumbShadowPath); translatedThumbShadowPath.transform(thumbShadowMatrix); ca...
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private void setNormalizedMinValue(double value) { normalizedMinValue = Math.max(0d, Math.min(1d, Math.min(value, normalizedMaxValue))); invalidate(); }
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private void setNormalizedMaxValue(double value) { normalizedMaxValue = Math.max(0d, Math.min(1d, Math.max(value, normalizedMinValue))); invalidate(); }
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@SuppressWarnings("unchecked") protected T normalizedToValue(double normalized) { double v = absoluteMinValuePrim + normalized * (absoluteMaxValuePrim - absoluteMinValuePrim); // TODO parameterize this rounding to allow variable decimal points return (T) numberType.toNumber(Math.round(v * 10...
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protected double valueToNormalized(T value) { if (0 == absoluteMaxValuePrim - absoluteMinValuePrim) { // prevent division by zero, simply return 0. return 0d; } return (value.doubleValue() - absoluteMinValuePrim) / (absoluteMaxValuePrim - absoluteMinValuePrim); }
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private double screenToNormalized(float screenCoord) { int width = getWidth(); if (width <= 2 * padding) { // prevent division by zero, simply return 0. return 0d; } else { double result = (screenCoord - padding) / (width - 2 * padding); return Mat...
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public static <K> void updateWeights(double l2, double learningRate, Map<K, Double> weights, Map<K, Double> newWeights) { if(l2 > 0.0) { for(Map.Entry<K, Double> e : weights.entrySet()) { K column = e.getKey(); newWeights.put(column, newWeights.get(column) + l2*e.getV...
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public static <K> double estimatePenalty(double l2, Map<K, Double> weights) { double penalty = 0.0; if(l2 > 0.0) { double sumWeightsSquared = 0.0; for(double w : weights.values()) { sumWeightsSquared += w*w; } penalty = l2*sumWeightsSquared...
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