idx int64 0 41.2k | question stringlengths 74 4.04k | target stringlengths 7 750 |
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36,700 | 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 ) + " has no " + name + " attribute" ... | Get an Attribute from the given node and throwing an exception in the case it is required but not present |
36,701 | 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 > ( ) { public Iterator < Node > iterator ( ) { r... | evaluates a XPath expression and loops over the nodeset result |
36,702 | public String getProperty ( String key , String defaultValue ) { String value = resolver . get ( key ) ; return ( value == null ) ? defaultValue : value ; } | Returns the configuration property for the given key or the given default value . |
36,703 | public static ConfigurationOption newConfiguration ( String pid ) { return new org . ops4j . pax . exam . cm . internal . ConfigurationProvisionOption ( pid , new HashMap < String , Object > ( ) ) ; } | Creates a basic empty configuration for the given PID |
36,704 | public static ConfigurationOption overrideConfiguration ( String pid ) { return new org . ops4j . pax . exam . cm . internal . ConfigurationProvisionOption ( pid , new HashMap < String , Object > ( ) ) . override ( true ) . create ( false ) ; } | Creates an overriding empty configuration for the given PID |
36,705 | public static ConfigurationOption factoryConfiguration ( String pid ) { return new org . ops4j . pax . exam . cm . internal . ConfigurationProvisionOption ( pid , new HashMap < String , Object > ( ) ) . factory ( true ) ; } | Creates a factory empty configuration for the given PID |
36,706 | 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 file : files ) { if (... | read all configuration files from a folder and transform them into configuration options |
36,707 | 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 ( ) >= endTime ) { throw new TestContainerExceptio... | Retrieve bundle context from given bundle . If the bundle is being restarted the bundle context can be null for some time |
36,708 | public EntityManager getEntityManager ( EntityManagerFactory emf ) { log . debug ( "producing EntityManager" ) ; return emf . createEntityManager ( ) ; } | Use a producer method so that CDI will find this EntityManager . |
36,709 | public TestProbeBuilder createProbeBuilder ( Object testClassInstance ) throws IOException , ExamConfigurationException { if ( defaultProbeBuilder == null ) { defaultProbeBuilder = system . createProbe ( ) ; } TestProbeBuilder probeBuilder = overwriteWithUserDefinition ( currentTestClass , testClassInstance ) ; if ( pr... | Lazily creates a probe builder . The same probe builder will be reused for all test classes unless the default builder is overridden in a given class . |
36,710 | 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 . currentTimeMillis ( ) ; lo... | Copy a stream to a destination . It does not close the streams . |
36,711 | 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 ) ; } finally { if ( is != null ) { is . cl... | Copy a stream from an urlto a destination . |
36,712 | public void close ( ) throws IOException { if ( jarOutputStream != null ) { jarOutputStream . close ( ) ; } else if ( os != null ) { os . close ( ) ; } } | Closes the archive and releases file system resources . No more files or directories may be added after calling this method . |
36,713 | private void addDirectory ( File root , File directory , String targetPath , ZipOutputStream zos ) throws IOException { String prefix = targetPath ; if ( ! prefix . isEmpty ( ) && ! prefix . endsWith ( "/" ) ) { prefix += "/" ; } if ( ! directory . equals ( root ) ) { String path = normalizePath ( root , directory ) ; ... | Recursively adds the contents of the given directory and all subdirectories to the given ZIP output stream . |
36,714 | 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 ) ; ... | Adds a given file to the given ZIP output stream . |
36,715 | private String normalizePath ( File root , File file ) { String relativePath = file . getPath ( ) . substring ( root . getPath ( ) . length ( ) + 1 ) ; String path = relativePath . replaceAll ( "\\" + File . separator , "/" ) ; return path ; } | Returns the relative path of the given file with respect to the root directory with all file separators replaced by slashes . |
36,716 | public void copyBootClasspathLibraries ( ) throws IOException { BootClasspathLibraryOption [ ] bootClasspathLibraryOptions = subsystem . getOptions ( BootClasspathLibraryOption . class ) ; for ( BootClasspathLibraryOption bootClasspathLibraryOption : bootClasspathLibraryOptions ) { UrlReference libraryUrl = bootClasspa... | Copy jars specified as BootClasspathLibraryOption in system to the karaf lib path to make them available in the boot classpath |
36,717 | 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 : opti... | Copy dependencies specified as ProvisionOption in system to the deploy folder |
36,718 | 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" ) ; writeDependenciesFeature ( wr , subsystem . getOp... | Create a feature for the test dependencies specified as ProvisionOption in the system |
36,719 | static void writeDependenciesFeature ( Writer writer , ProvisionOption < ? > ... provisionOptions ) { XMLOutputFactory xof = XMLOutputFactory . newInstance ( ) ; xof . setProperty ( "javax.xml.stream.isRepairingNamespaces" , true ) ; XMLStreamWriter sw = null ; try { sw = xof . createXMLStreamWriter ( writer ) ; sw . w... | Write a feature xml structure for test dependencies specified as ProvisionOption in system to the given writer |
36,720 | 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 ( ) . indexOf ( ".tar.gz" ) > 0 )... | Extract zip or tar . gz archives to a target folder |
36,721 | 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 , comma... | Appends an array of strings to command line . |
36,722 | public CommandLineBuilder append ( final String segment ) { if ( segment != null && ! segment . isEmpty ( ) ) { return append ( new String [ ] { segment } ) ; } return this ; } | Appends a string to command line . |
36,723 | 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 . class . getClassLoader ( ) . getResource ... | Gets the artifact version out of dependencies file . The dependencies file had to be generated by using the maven plugin . |
36,724 | public static MavenArtifactUrlReference . VersionResolver asInProject ( ) { return new MavenArtifactUrlReference . VersionResolver ( ) { public String getVersion ( final String groupId , final String artifactId ) { return getArtifactVersion ( groupId , artifactId ) ; } } ; } | Utility method for creating an artifact version resolver that will get the version out of maven project . |
36,725 | 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" ) ; ZipBuilder builder = new ZipBuilder ( probeWar ) ; ... | Builds a WAR from the given option . |
36,726 | 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 ] ; } } | constant times a vector plus a vector |
36,727 | 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 ; } | returns the dot product of two vectors |
36,728 | private static double euclideanNorm ( double vector [ ] ) { int n = vector . length ; if ( n < 1 ) { return 0 ; } if ( n == 1 ) { return Math . abs ( vector [ 0 ] ) ; } double scale = 0 ; double sum = 1 ; for ( int i = 0 ; i < n ; i ++ ) { if ( vector [ i ] != 0 ) { double abs = Math . abs ( vector [ i ] ) ; if ( scale... | returns the euclidean norm of a vector |
36,729 | private static void scale ( double constant , double vector [ ] ) { if ( constant == 1.0 ) return ; for ( int i = 0 ; i < vector . length ; i ++ ) { vector [ i ] *= constant ; } } | scales a vector by a constant |
36,730 | @ SuppressWarnings ( "unused" ) public void setAutoScaleEnabled ( boolean isAutoScaleEnabled ) { this . isAutoScaleEnabled = isAutoScaleEnabled ; for ( int i = 0 , size = foldableItemsMap . size ( ) ; i < size ; i ++ ) { foldableItemsMap . valueAt ( i ) . setAutoScaleEnabled ( isAutoScaleEnabled ) ; } } | Sets whether view should scale down to fit moving part into screen . |
36,731 | public void setFoldRotation ( float rotation ) { foldRotation = rotation ; topPart . applyFoldRotation ( rotation ) ; bottomPart . applyFoldRotation ( rotation ) ; setInTransformation ( rotation != 0f ) ; scaleFactor = 1f ; if ( isAutoScaleEnabled && width > 0 ) { double sin = Math . abs ( Math . sin ( Math . toRadians... | Fold rotation value in degrees . |
36,732 | public void setRollingDistance ( float distance ) { final float scaleY = scale * scaleFactor * scaleFactorY ; topPart . applyRollingDistance ( distance , scaleY ) ; bottomPart . applyRollingDistance ( distance , scaleY ) ; } | Translation preserving middle line splitting . |
36,733 | public void unfold ( View coverView , View detailsView ) { if ( this . coverView == coverView && this . detailsView == detailsView ) { scrollToPosition ( 1 ) ; return ; } if ( ( this . coverView != null && this . coverView != coverView ) || ( this . detailsView != null && this . detailsView != detailsView ) ) { schedul... | Starting unfold animation for given views . |
36,734 | 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 ) ; retu... | Return the last point of the ST_Linestring . |
36,735 | public long getId ( double x , double y ) { double down = ( extentMax - y ) / binSize ; double over = ( x - extentMin ) / binSize ; return ( ( long ) down * numCols ) + ( long ) over ; } | Gets bin ID from a point . |
36,736 | 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 , ymin , xmax... | Gets the envelope for the bin ID . |
36,737 | 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 ; enve... | Gets the envelope for the bin that contains the x y coords . |
36,738 | public boolean next ( LongWritable key , Text value ) throws IOException { JsonToken token ; if ( parser == null ) { parser = new JsonFactory ( ) . createJsonParser ( inputStream ) ; parser . setCodec ( new ObjectMapper ( ) ) ; token = parser . nextToken ( ) ; while ( token != null && ! ( token == JsonToken . START_ARR... | Both Esri JSON and GeoJSON conveniently have features |
36,739 | 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 ) ) ) ; } | Log when comparing geometries in different spatial references |
36,740 | public static int getWKID ( BytesWritable geomref ) { ByteBuffer bb = ByteBuffer . wrap ( geomref . getBytes ( ) ) ; return bb . getInt ( 0 ) ; } | Gets the WKID for the given hive geometry bytes |
36,741 | protected boolean moveToRecordStart ( ) throws IOException { int next = 0 ; long resetPosition = readerPosition ; while ( true ) { while ( next != '{' ) { next = getChar ( ) ; if ( next < 0 ) { return false ; } } resetPosition = readerPosition ; inputReader . mark ( 100 ) ; next = getNonWhite ( ) ; if ( next < 0 ) { re... | Given an arbitrary byte offset into a unenclosed JSON document find the start of the next record in the document . Discard trailing bytes from the previous record if we happened to seek to the middle of it |
36,742 | public float getProgress ( ) throws IOException { if ( reachedEnd ) return 1 ; else { final long filePos = in . position ( ) ; final long fileEnd = virtualEnd >>> 16 ; return ( float ) ( filePos - fileStart ) / ( fileEnd - fileStart + 1 ) ; } } | Unless the end has been reached this only takes file position into account not the position within the block . |
36,743 | 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 ; if ( n >>> 8 == BGZF_MAGIC << 8 >>> 8 ) ++ p ; else if ( n >>> 16 == BGZF_MAGIC << 16 >>> 16 ) p += 2 ; ... | Returns a negative number if it doesn t find anything . |
36,744 | private static void writeTerminatorBlock ( final OutputStream out , final SAMFormat samOutputFormat ) throws IOException { if ( SAMFormat . CRAM == samOutputFormat ) { CramIO . issueEOF ( CramVersions . DEFAULT_CRAM_VERSION , out ) ; } else if ( SAMFormat . BAM == samOutputFormat ) { out . write ( BlockCompressedStream... | Terminate the aggregated output stream with an appropriate SAMOutputFormat - dependent terminator block |
36,745 | public static < T extends Locatable > void setIntervals ( Configuration conf , List < T > intervals ) { setTraversalParameters ( conf , intervals , false ) ; } | Only include reads that overlap the given intervals . Unplaced unmapped reads are not included . |
36,746 | public static void unsetTraversalParameters ( Configuration conf ) { conf . unset ( BOUNDED_TRAVERSAL_PROPERTY ) ; conf . unset ( INTERVALS_PROPERTY ) ; conf . unset ( TRAVERSE_UNPLACED_UNMAPPED_PROPERTY ) ; } | Reset traversal parameters so that all reads are included . |
36,747 | static QueryInterval [ ] prepareQueryIntervals ( final List < Interval > rawIntervals , final SAMSequenceDictionary sequenceDictionary ) { if ( rawIntervals == null || rawIntervals . isEmpty ( ) ) { return null ; } final QueryInterval [ ] convertedIntervals = rawIntervals . stream ( ) . map ( rawInterval -> convertSimp... | Converts a List of SimpleIntervals into the format required by the SamReader query API |
36,748 | 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... | Converts an interval in SimpleInterval format into an htsjdk QueryInterval . |
36,749 | 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 . getL... | Convert quality scores in - place . |
36,750 | public static int verifyQuality ( Text quality , BaseQualityEncoding encoding ) { int max , min ; if ( encoding == BaseQualityEncoding . Illumina ) { max = FormatConstants . ILLUMINA_OFFSET + FormatConstants . ILLUMINA_MAX ; min = FormatConstants . ILLUMINA_OFFSET ; } else if ( encoding == BaseQualityEncoding . Sanger ... | Verify that the given quality bytes are within the range allowed for the specified encoding . |
36,751 | 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 ... | Writes some statistics about each BGZF block index file given as an argument . |
36,752 | 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 ) ; } | first statement ... |
36,753 | 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 -> exc... | Returns all the files in a directory that match the given pattern and that don t have the given extension . |
36,754 | static void mergeInto ( List < Path > parts , OutputStream out ) throws IOException { for ( final Path part : parts ) { Files . copy ( part , out ) ; Files . delete ( part ) ; } } | Merge the given part files in order into an output stream . This deletes the parts . |
36,755 | public List < InputSplit > getSplits ( JobContext job ) throws IOException { final List < InputSplit > splits = super . getSplits ( job ) ; Collections . sort ( splits , new Comparator < InputSplit > ( ) { public int compare ( InputSplit a , InputSplit b ) { FileSplit fa = ( FileSplit ) a , fb = ( FileSplit ) b ; retur... | The splits returned are FileSplits . |
36,756 | public static WrapSeekable < FSDataInputStream > openPath ( FileSystem fs , Path p ) throws IOException { return new WrapSeekable < FSDataInputStream > ( fs . open ( p ) , fs . getFileStatus ( p ) . getLen ( ) , p ) ; } | A helper for the common use case . |
36,757 | 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 ) . setUseAs... | Does not close the stream . |
36,758 | 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 ) { int load... | Skip n bytes from the InputStream . |
36,759 | 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 ; } return ( float ) ( ( bci . getFilePointer ( ) >>> 16 ) - fileStart ) / ( length + 1 ) ; } | For compressed BCF unless the end has been reached this is quite inaccurate . |
36,760 | public void processAlignment ( final SAMRecord rec ) throws IOException { if ( count == 0 || ( count + 1 ) % granularity == 0 ) { SAMFileSource fileSource = rec . getFileSource ( ) ; SAMFileSpan filePointer = fileSource . getFilePointer ( ) ; writeVirtualOffset ( getPos ( filePointer ) ) ; } count ++ ; } | Process the given record for the index . |
36,761 | public void writeVirtualOffset ( long virtualOffset ) throws IOException { lb . put ( 0 , virtualOffset ) ; out . write ( byteBuffer . array ( ) ) ; } | Write the given virtual offset to the index . This method is for internal use only . |
36,762 | 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 ) ; final LongBuffer lb = byteBuffer ... | Perform indexing on the given BAM file at the granularity level specified . |
36,763 | 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 ImmutableList . of ( ) ; } final List ... | Returns the list of intervals found in a string configuration property separated by colons . |
36,764 | 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 ; } | Inexact due to the nature of virtual offsets . |
36,765 | private void fixBCFSplits ( List < FileSplit > splits , List < InputSplit > newSplits ) throws IOException { Collections . sort ( splits , new Comparator < FileSplit > ( ) { public int compare ( FileSplit a , FileSplit b ) { return a . getPath ( ) . compareTo ( b . getPath ( ) ) ; } } ) ; for ( int i = 0 ; i < splits .... | FileVirtualSplits uncompressed in FileSplits . |
36,766 | public static boolean parseBoolean ( String value , boolean defaultValue ) { if ( value == null ) return defaultValue ; value = value . trim ( ) ; final String [ ] acceptedTrue = new String [ ] { "yes" , "true" , "t" , "y" , "1" } ; final String [ ] acceptedFalse = new String [ ] { "no" , "false" , "f" , "n" , "0" } ; ... | Convert a string to a boolean . |
36,767 | 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 .... | Writes some statistics about each splitting BAM index file given as an argument . |
36,768 | 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 ) ; } } } | When a network request is cancelled we stop tracking it and do not send the information through . Future updates may include sending the cancelled request timing through with information showing it was cancelled . |
36,769 | 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 ( ) . connectTimeout... | Raw post method that delivers a pre - built RUM payload to the Raygun API . |
36,770 | public static void init ( Context context ) { String apiKey = readApiKey ( context ) ; init ( context , apiKey ) ; } | Initializes the Raygun client . This expects that you have placed the API key in your AndroidManifest . xml in a meta - data element . |
36,771 | 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 ... | Initializes the Raygun client with your Android application s context and your Raygun API key . The version transmitted will be the value of the versionName attribute in your manifest element . |
36,772 | public static void init ( Context context , String apiKey , String version ) { init ( context , apiKey ) ; RaygunClient . version = version ; } | Initializes the Raygun client with your Android application s context your Raygun API key and the version of your application |
36,773 | 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... | Sends an exception - type object to Raygun with a list of tags you specify and a set of custom data . |
36,774 | 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 ( nam... | Sends a pulse timing event to Raygun . The message is sent on a background thread . |
36,775 | 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." )... | Registers a converter . |
36,776 | public static < T extends Tag , V > void unregister ( Class < T > tag , Class < V > type ) { tagToConverter . remove ( tag ) ; typeToConverter . remove ( type ) ; } | Unregisters a converter . |
36,777 | 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 no converte... | Converts the given tag to a value . |
36,778 | 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 < ? > clazz : getAllClass... | Converts the given value to a tag . |
36,779 | public static void writeTag ( OutputStream out , Tag tag ) throws IOException { writeTag ( out , tag , false ) ; } | Writes an NBT tag in big endian . |
36,780 | public void setValue ( List < Tag > value ) throws IllegalArgumentException { this . type = null ; this . value . clear ( ) ; for ( Tag tag : value ) { this . add ( tag ) ; } } | Sets the value of this tag . The list tag s type will be set to that of the first tag being added or null if the given list is empty . |
36,781 | public boolean add ( Tag tag ) throws IllegalArgumentException { if ( tag == null ) { return false ; } if ( this . type == null ) { this . type = tag . getClass ( ) ; } else if ( tag . getClass ( ) != this . type ) { throw new IllegalArgumentException ( "Tag type cannot differ from ListTag type." ) ; } return this . va... | Adds a tag to this list tag . If the list does not yet have a type it will be set to the type of the tag being added . |
36,782 | public void setValue ( Map < String , Tag > value ) { this . value = new LinkedHashMap < String , Tag > ( value ) ; } | Sets the value of this tag . |
36,783 | public < T extends Tag > T get ( String tagName ) { return ( T ) this . value . get ( tagName ) ; } | Gets the tag with the specified name . |
36,784 | public < T extends Tag > T put ( T tag ) { return ( T ) this . value . put ( tag . getName ( ) , tag ) ; } | Puts the tag into this compound tag . |
36,785 | public < T extends Tag > T remove ( String tagName ) { return ( T ) this . value . remove ( tagName ) ; } | Removes a tag from this compound tag . |
36,786 | 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 \"" + tag . getSimpleNam... | Registers a tag class . |
36,787 | public static Class < ? extends Tag > getClassFor ( int id ) { if ( ! idToTag . containsKey ( id ) ) { return null ; } return idToTag . get ( id ) ; } | Gets the tag class with the given id . |
36,788 | public static int getIdFor ( Class < ? extends Tag > clazz ) { if ( ! tagToId . containsKey ( clazz ) ) { return - 1 ; } return tagToId . get ( clazz ) ; } | Gets the id of the given tag class . |
36,789 | 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 > constructor = clazz . getDeclaredCo... | Creates an instance of the tag with the given id using the String constructor . |
36,790 | 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 ( ) + ( ! showTextAboveThumbs ? 0 : Pixel... | Ensures correct size of the widget . |
36,791 | private void drawThumb ( float screenCoord , boolean pressed , Canvas canvas , boolean areSelectedValuesDefault ) { Bitmap buttonToDraw ; if ( ! activateOnDefaultValues && areSelectedValuesDefault ) { buttonToDraw = thumbDisabledImage ; } else { buttonToDraw = pressed ? thumbPressedImage : thumbImage ; } canvas . drawB... | Draws the normal resp . pressed thumb image on specified x - coordinate . |
36,792 | private void drawThumbShadow ( float screenCoord , Canvas canvas ) { thumbShadowMatrix . setTranslate ( screenCoord + thumbShadowXOffset , textOffset + thumbHalfHeight + thumbShadowYOffset ) ; translatedThumbShadowPath . set ( thumbShadowPath ) ; translatedThumbShadowPath . transform ( thumbShadowMatrix ) ; canvas . dr... | Draws a drop shadow beneath the slider thumb . |
36,793 | private void setNormalizedMinValue ( double value ) { normalizedMinValue = Math . max ( 0d , Math . min ( 1d , Math . min ( value , normalizedMaxValue ) ) ) ; invalidate ( ) ; } | Sets normalized min value to value so that 0 < = value < = normalized max value < = 1 . The View will get invalidated when calling this method . |
36,794 | private void setNormalizedMaxValue ( double value ) { normalizedMaxValue = Math . max ( 0d , Math . min ( 1d , Math . max ( value , normalizedMinValue ) ) ) ; invalidate ( ) ; } | Sets normalized max value to value so that 0 < = normalized min value < = value < = 1 . The View will get invalidated when calling this method . |
36,795 | @ SuppressWarnings ( "unchecked" ) protected T normalizedToValue ( double normalized ) { double v = absoluteMinValuePrim + normalized * ( absoluteMaxValuePrim - absoluteMinValuePrim ) ; return ( T ) numberType . toNumber ( Math . round ( v * 100 ) / 100d ) ; } | Converts a normalized value to a Number object in the value space between absolute minimum and maximum . |
36,796 | protected double valueToNormalized ( T value ) { if ( 0 == absoluteMaxValuePrim - absoluteMinValuePrim ) { return 0d ; } return ( value . doubleValue ( ) - absoluteMinValuePrim ) / ( absoluteMaxValuePrim - absoluteMinValuePrim ) ; } | Converts the given Number value to a normalized double . |
36,797 | private double screenToNormalized ( float screenCoord ) { int width = getWidth ( ) ; if ( width <= 2 * padding ) { return 0d ; } else { double result = ( screenCoord - padding ) / ( width - 2 * padding ) ; return Math . min ( 1d , Math . max ( 0d , result ) ) ; } } | Converts screen space x - coordinates into normalized values . |
36,798 | 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 . getVa... | Updates the weights by applying the L2 regularization . |
36,799 | 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 / 2.0 ; } return penalty ; } | Estimates the penalty by adding the L2 regularization . |
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