idx int64 0 41.2k | question stringlengths 73 5.81k | target stringlengths 5 918 |
|---|---|---|
40,600 | private boolean matchletMagicCompare ( int offset , byte [ ] data ) { if ( oneMatchletMagicEquals ( offset , data ) ) { int nChildren = content . getInt ( offset + 24 ) ; if ( nChildren > 0 ) { int firstChildOffset = content . getInt ( offset + 28 ) ; return matchletMagicCompareOr ( nChildren , firstChildOffset , data ... | Returns whether data satisfies the matchlet and its children . |
40,601 | private boolean isRetryable ( Exception e ) { final String mName = "isRetryable" ; String exClassName = e . getClass ( ) . getName ( ) ; boolean retVal = containsException ( _retryIncludeExceptions , e ) && ! containsException ( _retryExcludeExceptions , e ) ; if ( logger . isLoggable ( Level . FINE ) ) logger . logp (... | Check the retryable exception lists to determine whether the given Exception is retryable . |
40,602 | public void registerPlatformMode ( PlatformMode mode ) { platformMode = mode ; if ( mode . equals ( PlatformMode . EE ) ) { logger . config ( "Batch configured in EE mode by SPI, taking precedence over properties file" ) ; } else if ( mode . equals ( PlatformMode . SE ) ) { logger . config ( "Batch configured in SE mod... | Override properties - file based config with programmatic setting of SE or EE platform mode . |
40,603 | private boolean isSkippable ( Exception e ) { final String mName = "isSkippable" ; String exClassName = e . getClass ( ) . getName ( ) ; boolean retVal = containsSkippable ( _skipIncludeExceptions , e ) && ! containsSkippable ( _skipExcludeExceptions , e ) ; if ( logger . isLoggable ( Level . FINE ) ) logger . logp ( L... | Check the skipCount and skippable exception lists to determine whether the given Exception is skippable . |
40,604 | private boolean containsSkippable ( Set < String > skipList , Exception e ) { final String mName = "containsSkippable" ; boolean retVal = false ; for ( Iterator it = skipList . iterator ( ) ; it . hasNext ( ) ; ) { String exClassName = ( String ) it . next ( ) ; try { ClassLoader tccl = Thread . currentThread ( ) . get... | Check whether given exception is in skippable exception list |
40,605 | private Object processItem ( Object itemRead ) { logger . entering ( sourceClass , "processItem" , itemRead ) ; Object processedItem = null ; if ( processorProxy == null ) { return itemRead ; } try { for ( ItemProcessListenerProxy processListenerProxy : itemProcessListeners ) { processListenerProxy . beforeProcess ( it... | Process an item previously read by the reader |
40,606 | private void initPlatformSEorEE ( ) { String seMode = serviceImplClassNames . get ( Name . JAVA_EDITION_IS_SE_DUMMY_SERVICE ) ; if ( seMode . equalsIgnoreCase ( "true" ) ) { platformMode = PlatformMode . SE ; batchConfigImpl . setJ2seMode ( true ) ; } else { platformMode = PlatformMode . EE ; batchConfigImpl . setJ2seM... | Push hardened config value onto batchConfigImpl and cache the value in a field . |
40,607 | public static synchronized Schema getXJCLSchema ( ) { if ( schema == null ) { try { URL url = ValidatorHelper . class . getResource ( "/" + SCHEMA_LOCATION ) ; schema = sf . newSchema ( url ) ; } catch ( SAXException e ) { throw new RuntimeException ( e ) ; } } return schema ; } | This method must be synchronized as SchemaFactory is not thread - safe |
40,608 | private void buildSubJobBatchWorkUnits ( ) { List < Flow > flows = this . split . getFlows ( ) ; parallelBatchWorkUnits = new ArrayList < BatchFlowInSplitWorkUnit > ( ) ; synchronized ( subJobs ) { for ( Flow flow : flows ) { subJobs . add ( PartitionedStepBuilder . buildFlowInSplitSubJob ( jobContext , this . split , ... | Note we restart all flows . There is no concept of the flow completed . It is only steps within the flows that may have already completed and so may not have needed to be rerun . |
40,609 | private static void initializeWithDefaultScope ( ) { try { Class < ? > aClass = Class . forName ( DEFAULT_SCOPE_FACTORY ) ; INSTANCE = ( SingletonProvider ) aClass . newInstance ( ) ; } catch ( Exception e ) { throw new RuntimeException ( e ) ; } } | Initialize with the default instance |
40,610 | public static void initialize ( SingletonProvider instance ) { synchronized ( SingletonProvider . class ) { if ( INSTANCE == null ) { INSTANCE = instance ; } else { throw new RuntimeException ( "SingletonProvider is already initialized with " + INSTANCE ) ; } } } | Initialize with an explicit instance |
40,611 | private List < GraphResult > getPcaData ( double [ ] [ ] data , BiMap < Integer , String > dataNames ) { int rows = data . length ; int cols = data . length ; double matrixSum = 0 ; double [ ] rowSums = new double [ rows ] ; for ( int i = 0 ; i < rows ; i ++ ) { for ( int j = 0 ; j < cols ; j ++ ) { matrixSum += data [... | Convert the similarity matrix to an Eigen matrix . |
40,612 | public void addBin ( List < Chunk > chunksToAdd , long lastLocus ) { assert chunks != null ; contig = new Contig ( contig . referenceName , contig . start , lastLocus ) ; chunks . addAll ( chunksToAdd ) ; updateSpan ( ) ; } | Appends chunks from another bin to the list and moved the end position . |
40,613 | public long finish ( ) { final BAMIndexContent content = indexBuilder . processReference ( referenceIndex ) ; outputWriter . writeReference ( content ) ; outputWriter . close ( ) ; return indexBuilder . getNoCoordinateRecordCount ( ) ; } | Finalizes writing and closes the file . |
40,614 | static Interval gridSearch ( UnivariateFunction fn , double start , double end , double step ) { double lowMax = start ; double alphaMax = start - step ; double likMax = 0.0 ; double lastAlpha = start ; double alpha = start ; while ( alpha < end ) { double likelihood = fn . value ( alpha ) ; if ( alphaMax < start || li... | Runs a grid search for the maximum value of a univariate function . |
40,615 | public static double maximize ( UnivariateFunction fn , double gridStart , double gridEnd , double gridStep , double relErr , double absErr , int maxIter , int maxEval ) { Interval interval = gridSearch ( fn , gridStart , gridEnd , gridStep ) ; BrentOptimizer bo = new BrentOptimizer ( relErr , absErr ) ; UnivariatePoin... | Maximizes a univariate function using a grid search followed by Brent s algorithm . |
40,616 | static boolean passesFilter ( SAMRecord record , Filter filter , String referenceName ) { if ( filter == Filter . UNMAPPED_ONLY && ! record . getReadUnmappedFlag ( ) ) { return false ; } if ( filter == Filter . MAPPED_ONLY && record . getReadUnmappedFlag ( ) ) { return false ; } final boolean referenceNameMismatch = re... | Checks if the record matches our filter . |
40,617 | public void writeReference ( final BAMIndexContent content ) { if ( content == null ) { writeNullContent ( ) ; return ; } final BAMIndexContent . BinList bins = content . getBins ( ) ; final int size = bins == null ? 0 : content . getNumberOfNonNullBins ( ) ; if ( size == 0 ) { writeNullContent ( ) ; return ; } final B... | Write this content as binary output |
40,618 | private void writeChunkMetaData ( final BAMIndexMetaData metaData ) { codec . writeInt ( GenomicIndexUtil . MAX_BINS ) ; final int nChunk = 2 ; codec . writeInt ( nChunk ) ; codec . writeLong ( metaData . getFirstOffset ( ) ) ; codec . writeLong ( metaData . getLastOffset ( ) ) ; codec . writeLong ( metaData . getAlign... | Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450 |
40,619 | public double similarity ( VariantCall call1 , VariantCall call2 ) { int minNumberOfGenotypes = Math . min ( call1 . getGenotypeCount ( ) , call2 . getGenotypeCount ( ) ) ; int numberOfSharedAlleles = 0 ; for ( int i = 0 ; i < minNumberOfGenotypes ; ++ i ) { if ( call1 . getGenotype ( i ) == call2 . getGenotype ( i ) )... | scores when the number of alleles is different than 2 and when the genotypes are unphased . |
40,620 | public static List < ReadBaseWithReference > extractReadBases ( Read read ) { if ( ! read . hasAlignment ( ) || ( read . getAlignment ( ) . getCigarCount ( ) == 0 ) ) { return null ; } ImmutableList . Builder < ReadBaseWithReference > bases = ImmutableList . builder ( ) ; String readSeq = read . getAlignedSequence ( ) ... | Use the given read to build a list of aligned read and reference base information . |
40,621 | private static double pGenotype ( Genotype g , double refProb ) { switch ( g ) { case REF_HOMOZYGOUS : return refProb * refProb ; case HETEROZYGOUS : return refProb * ( 1.0 - refProb ) ; case NONREF_HOMOZYGOUS : return ( 1.0 - refProb ) * ( 1.0 - refProb ) ; default : throw new IllegalArgumentException ( "Illegal genot... | Compute the probability of a genotype given the reference allele probability . |
40,622 | private static double probObsGivenTruth ( Base observed , Genotype trueGenotype , ReadStatus trueStatus ) { return P_OBS_GIVEN_TRUTH . get ( toTableIndex ( observed , trueGenotype , trueStatus ) ) ; } | Look up the probability of an observation conditioned on the underlying state . |
40,623 | public double value ( double alpha ) { double logLikelihood = 0.0 ; for ( ReadCounts rc : readCounts . values ( ) ) { double refProb = rc . getRefFreq ( ) ; double pPosition = 0.0 ; for ( Genotype trueGenotype1 : Genotype . values ( ) ) { double pGenotype1 = pGenotype ( trueGenotype1 , refProb ) ; for ( Genotype trueGe... | Compute the likelihood of a contaminant fraction alpha . |
40,624 | public static PCollection < Read > getReadsFromBAMFileSharded ( Pipeline p , PipelineOptions pipelineOptions , OfflineAuth auth , List < Contig > contigs , ReaderOptions options , String BAMFile , ShardingPolicy shardingPolicy ) throws IOException { ReadBAMTransform readBAMSTransform = new ReadBAMTransform ( options ) ... | Get reads from a single BAM file by serially reading one shard at a time . |
40,625 | public void addFile ( String loaderPath , URL file ) { List list = ( List ) filesMap . get ( loaderPath ) ; if ( list == null ) { list = new ArrayList ( ) ; filesMap . put ( loaderPath , list ) ; } list . add ( file ) ; } | add a file to the given loader |
40,626 | public static final void releaseMultiple ( CMutex mutex [ ] ) { Arrays . sort ( mutex , new CMutexComparator ( ) ) ; for ( int i = mutex . length - 1 ; i >= 0 ; i -- ) { mutex [ i ] . release ( ) ; } } | Releases an array of mutex previously acquired |
40,627 | public final void release ( ) { synchronized ( this . LOCK ) { if ( ( this . owner != null ) && ( this . owner . get ( ) == Thread . currentThread ( ) ) ) { this . acquire -- ; if ( this . acquire == 0 ) { this . owner = null ; this . LOCK . notify ( ) ; } return ; } if ( ( this . owner != null ) && ( this . owner . ge... | Releases the mutex |
40,628 | private static boolean isDescendant ( final Node n , final Node ref ) { if ( ref == null ) { return false ; } if ( n == ref ) { return true ; } NodeList nl = ref . getChildNodes ( ) ; for ( int i = 0 ; i < nl . getLength ( ) ; i ++ ) { boolean result = isDescendant ( n , nl . item ( i ) ) ; if ( result ) { return resul... | return true if n is a descendant of ref |
40,629 | private static PbDocument [ ] getPbDocs ( final NodeList nl ) { List list = new ArrayList ( ) ; Element prevpb = null ; for ( int i = 0 ; i < nl . getLength ( ) ; i ++ ) { Element pb = ( Element ) nl . item ( i ) ; PbDocument pbdoc = new PbDocument ( prevpb , pb ) ; list . add ( pbdoc ) ; prevpb = pb ; if ( i == ( nl .... | Return the pagebreaks |
40,630 | private static void copyHeader ( final Document doc , final Document ndoc ) { NodeList headnl = doc . getElementsByTagName ( "head" ) ; if ( headnl . getLength ( ) > 0 ) { Element head = ( Element ) headnl . item ( 0 ) ; ndoc . getDocumentElement ( ) . insertBefore ( ndoc . adoptNode ( head . cloneNode ( true ) ) , ndo... | Copy the html header from doc to ndoc |
40,631 | private static String getParameter ( final String args [ ] , final String name ) { for ( int i = 0 ; i < args . length ; i ++ ) { if ( args [ i ] . equals ( name ) ) { if ( ( i + 1 ) < args . length ) { return args [ i + 1 ] ; } break ; } } return null ; } | Return the value of the given parameter if set |
40,632 | private static boolean hasParameter ( final String args [ ] , final String name ) { for ( int i = 0 ; i < args . length ; i ++ ) { if ( args [ i ] . equals ( name ) ) { return true ; } } return false ; } | return true if the given parameter is on the command line |
40,633 | private static void showUsage ( final String message ) { if ( message != null ) { System . out . println ( message ) ; } System . out . println ( "Usage :\n\tjava -cp yahp-sample.jar:yahp.jar org.allcolor.yahp.sample.CSimpleConversion" + " --url [http|file]://myuri --out /path/to.pdf [font options] [renderer options] [... | Show the usage of the tool |
40,634 | public void addClassPreload ( final String path , final byte array [ ] ) { try { this . preload . put ( path , new SoftReference ( new CGCCleaner ( path , array ) ) ) ; } catch ( Exception ignore ) { } } | add a class byte representation in the preload map |
40,635 | public static final CThreadContext getInstance ( ) { SoftReference ref = ( SoftReference ) CThreadContext . contextLocal . get ( Thread . currentThread ( ) ) ; CThreadContext context = null ; if ( ( ref == null ) || ( ref . get ( ) == null ) ) { context = new CThreadContext ( ) ; ref = new SoftReference ( context ) ; C... | Return a thread context |
40,636 | public final Object get ( String key ) { try { this . mutex . acquire ( ) ; return this . valueMap . get ( key ) ; } finally { try { this . mutex . release ( ) ; } catch ( Exception ignore ) { } } } | Get the value with the given key from this context |
40,637 | public final void set ( String key , Object value ) { try { this . mutex . acquire ( ) ; if ( value == null ) { this . valueMap . remove ( key ) ; } else { this . valueMap . put ( key , value ) ; } } finally { try { this . mutex . release ( ) ; } catch ( Exception ignore ) { } } } | Set a value in this context |
40,638 | public final String replaceExpr ( String message , String type ) { message = decode ( message ) ; List mapFilter = getFilter ( type ) ; if ( mapFilter == null ) return message ; Iterator it = mapFilter . iterator ( ) ; while ( it . hasNext ( ) ) { Object value [ ] = ( Object [ ] ) it . next ( ) ; String replacement = (... | Replace the input message using the rules type found in the xml configuration file |
40,639 | public static final CPadawan getInstance ( ) { try { mutex . acquire ( ) ; CPadawan toReturn = ( handle == null ) ? ( handle = new CPadawan ( ) ) : handle ; toReturn . init ( ) ; return toReturn ; } finally { try { mutex . release ( ) ; } catch ( Exception ignore ) { } } } | Return an instance of the padawan |
40,640 | private final List getFilter ( String type ) { try { mutex . acquire ( ) ; return ( List ) mapFilter . get ( type + ".filter" ) ; } finally { try { mutex . release ( ) ; } catch ( Throwable ignore ) { } } } | return the filters of type type |
40,641 | public final String validate ( String in , String type ) { CShaniDomParser parser = new CShaniDomParser ( ) ; Document doc = parser . parse ( new StringReader ( in ) , getTags ( type ) , getMerge ( type ) ) ; if ( doc != null ) return doc . toString ( ) ; else return in ; } | validate for xml the string in using the rules type type |
40,642 | public final String createEntityDeclaration ( ) throws UnsupportedEncodingException { StringBuffer buffer = new StringBuffer ( ) ; buffer . append ( "<!DOCTYPE padawan [\n" ) ; for ( int i = 0 ; i < entity . length ; i ++ ) { buffer . append ( "<!ENTITY " + entity [ i ] [ 1 ] + " '" + entity [ i ] [ 0 ] + "' >\n" ) ; }... | Create the padawan doctype |
40,643 | public final String getEntityDeclaration ( ) { if ( entityDecl == null ) try { entityDecl = createEntityDeclaration ( ) ; } catch ( Exception e ) { entityDecl = null ; } return entityDecl ; } | return the padawan doctype |
40,644 | public final String decode ( String toDecode ) { CEntityCoDec codec = new CEntityCoDec ( new HashMap ( ) ) ; return codec . decode ( toDecode ) ; } | decode entity in the string |
40,645 | public final String stringReplace ( String toBeReplaced , String toReplace , String replacement ) { Pattern pattern = Pattern . compile ( toReplace ) ; Matcher match = pattern . matcher ( toBeReplaced ) ; while ( match . find ( ) ) { toBeReplaced = match . replaceAll ( replacement ) ; match = pattern . matcher ( toBeRe... | A replace string method |
40,646 | private final boolean isAlone ( String tagName , String aloneTags [ ] ) { if ( aloneTags == null ) return false ; if ( tagName == null ) return false ; for ( int i = 0 ; i < aloneTags . length ; i ++ ) { if ( tagName . equalsIgnoreCase ( aloneTags [ i ] ) ) return true ; } return false ; } | return true if the given tag name is an empty tag |
40,647 | public final String escapeAttribute ( String in ) { in = escape ( in ) ; in = in . replaceAll ( "\"" , """ ) ; return in ; } | Escape the given string to be a valid content for an xml attribute |
40,648 | public final String escape ( String in ) { if ( in == null ) return "" ; if ( in . trim ( ) . equals ( "" ) ) return in ; if ( in . trim ( ) . length ( ) == 0 ) return in ; in = in . replaceAll ( "&" , "&" ) ; in = in . replaceAll ( "<" , "<" ) ; in = in . replaceAll ( ">" , ">" ) ; StringBuffer result = new ... | Escape the given string to be a valid content for an xml text node content |
40,649 | private static final CClassLoader createLoader ( final ClassLoader parent , final String name ) { try { return new CClassLoader ( parent , name ) ; } catch ( final Exception ignore ) { return null ; } } | Create a new loader |
40,650 | public static URL createMemoryURL ( final String entryName , final byte [ ] entry ) { try { final Class c = ClassLoader . getSystemClassLoader ( ) . loadClass ( "org.allcolor.yahp.converter.CMemoryURLHandler" ) ; final Method m = c . getDeclaredMethod ( "createMemoryURL" , new Class [ ] { String . class , byte [ ] . cl... | Creates and allocates a memory URL |
40,651 | private static List getClasses ( final File current , final List list ) { if ( current . isDirectory ( ) ) { try { list . add ( current . toURI ( ) . toURL ( ) ) ; } catch ( final Exception ignore ) { } final File children [ ] = current . listFiles ( ) ; for ( int i = 0 ; i < children . length ; i ++ ) { final File ele... | Return a list of classes and jar files |
40,652 | public static final CClassLoader getLoader ( final String fpath ) { String path = fpath ; CClassLoader currentLoader = CClassLoader . rootLoader ; if ( path == null ) { return CClassLoader . getRootLoader ( ) ; } if ( path . startsWith ( CClassLoader . ROOT_LOADER ) ) { path = path . substring ( 10 ) ; } final StringTo... | return the loader with the given path |
40,653 | public static final CClassLoader getRootLoader ( ) { if ( CClassLoader . rootLoader == null ) { CClassLoader . rootLoader = CClassLoader . createLoader ( CClassLoader . class . getClassLoader ( ) , CClassLoader . ROOT_LOADER ) ; } return CClassLoader . rootLoader ; } | return the rootloader |
40,654 | public static URL [ ] getURLs ( final String path ) { final File topDir = new File ( path ) ; final List list = new ArrayList ( ) ; CClassLoader . getClasses ( topDir , list ) ; final URL ret [ ] = new URL [ list . size ( ) + 1 ] ; for ( int i = 0 ; i < list . size ( ) ; i ++ ) { ret [ i ] = ( URL ) list . get ( i ) ; ... | Return a list of jar and classes located in path |
40,655 | public static final byte [ ] loadByteArray ( final InputStream in ) { try { final ByteArrayOutputStream bOut = new ByteArrayOutputStream ( ) ; final byte buffer [ ] = new byte [ 2048 ] ; int iNbByteRead = - 1 ; while ( ( iNbByteRead = in . read ( buffer ) ) != - 1 ) { bOut . write ( buffer , 0 , iNbByteRead ) ; } retur... | load the given inputstream in a byte array |
40,656 | public static final byte [ ] loadByteArray ( final URL urlToResource ) { InputStream in = null ; try { final URLConnection uc = urlToResource . openConnection ( ) ; uc . setUseCaches ( false ) ; in = uc . getInputStream ( ) ; return CClassLoader . loadByteArray ( in ) ; } catch ( final IOException ioe ) { return null ;... | load the given url in a byte array |
40,657 | private static final void loadResources ( final CClassLoader loader , final List URLList , final String resourceName ) { final List l = loader . getPrivateResource ( resourceName ) ; if ( l != null ) { URLList . addAll ( l ) ; } final List loaderList = new ArrayList ( ) ; for ( final Iterator it = loader . childrenMap ... | load multiple resources of same name |
40,658 | private static final void log ( final String Message , final int level ) { if ( ( level == CClassLoader . INFO ) && CClassLoader . log . isLoggable ( Level . INFO ) ) { CClassLoader . log . info ( Message ) ; } else if ( ( level == CClassLoader . DEBUG ) && CClassLoader . log . isLoggable ( Level . FINE ) ) { CClassLoa... | log the message |
40,659 | public static void releaseMemoryURL ( final URL u ) { try { final Class c = ClassLoader . getSystemClassLoader ( ) . loadClass ( "org.allcolor.yahp.converter.CMemoryURLHandler" ) ; final Method m = c . getDeclaredMethod ( "releaseMemoryURL" , new Class [ ] { URL . class } ) ; m . setAccessible ( true ) ; m . invoke ( n... | Release a previously allocated memory URL |
40,660 | private static final void setInit ( final CClassLoader loader ) { loader . booInit = true ; for ( final Iterator it = loader . getChildLoader ( ) ; it . hasNext ( ) ; ) { final Map . Entry entry = ( Map . Entry ) it . next ( ) ; CClassLoader . setInit ( ( CClassLoader ) entry . getValue ( ) ) ; } } | set the init flag of all loaders |
40,661 | private static final boolean sl ( final int level ) { if ( ( level == CClassLoader . INFO ) && CClassLoader . log . isLoggable ( Level . INFO ) ) { return true ; } else if ( ( level == CClassLoader . DEBUG ) && CClassLoader . log . isLoggable ( Level . FINE ) ) { return true ; } else if ( ( level == CClassLoader . FATA... | test if the logging level is enabled |
40,662 | private final void _destroy ( final Method logFactoryRelease ) { for ( final Iterator it = this . childrenMap . entrySet ( ) . iterator ( ) ; it . hasNext ( ) ; ) { final Map . Entry entry = ( Map . Entry ) it . next ( ) ; final CClassLoader loader = ( CClassLoader ) entry . getValue ( ) ; loader . _destroy ( logFactor... | Destroy instance variables . |
40,663 | public final void addClass ( final String className , final URL urlToClass ) { if ( ( className == null ) || ( urlToClass == null ) ) { return ; } if ( ! this . classesMap . containsKey ( className ) ) { this . classesMap . put ( className , urlToClass ) ; } } | add a class to known class |
40,664 | public final void addResource ( final String resouceName , final URL urlToResource ) { if ( ( urlToResource == null ) || ( resouceName == null ) ) { return ; } if ( this . resourcesMap . containsKey ( resouceName . replace ( '\\' , '/' ) ) ) { final Object to = this . resourcesMap . get ( resouceName . replace ( '\\' ,... | add a resource |
40,665 | private final CClassLoader getLoaderByName ( final String name ) { try { CClassLoader loader = ( CClassLoader ) this . childrenMap . get ( name ) ; if ( loader == null ) { loader = CClassLoader . createLoader ( this , name ) ; this . childrenMap . put ( name , loader ) ; } return loader ; } finally { try { } catch ( fi... | Return the child loader with the given name |
40,666 | private final List getPrivateResource ( final String name ) { try { final Object to = this . resourcesMap . get ( name ) ; final List list = new ArrayList ( ) ; if ( to instanceof URL ) { list . add ( ( URL ) to ) ; return list ; } else if ( to instanceof List ) { final List l = ( List ) to ; for ( int i = 0 ; i < l . ... | get the resource with the given name |
40,667 | private final String nGetLoaderPath ( ) { ClassLoader currentLoader = this ; final StringBuffer buffer = new StringBuffer ( ) ; buffer . append ( this . name ) ; while ( ( currentLoader = currentLoader . getParent ( ) ) != null ) { if ( currentLoader . getClass ( ) == CClassLoader . class ) { buffer . insert ( 0 , "/" ... | calculate the loader path |
40,668 | public final void reload ( final CClassLoaderConfig config ) { if ( this == CClassLoader . getRootLoader ( ) ) { return ; } if ( config == null ) { return ; } final CClassLoader parent = ( ( CClassLoader ) this . getParent ( ) ) ; parent . removeLoader ( this . name ) ; if ( this . isMandatory ( ) ) { CClassLoader . ma... | reload this loader |
40,669 | public final CClassLoader removeLoader ( final String loaderToRemove ) { if ( loaderToRemove . trim ( ) . length ( ) == 0 ) { throw new NullPointerException ( ) ; } return ( CClassLoader ) this . childrenMap . remove ( loaderToRemove ) ; } | remove the given loader from this loader |
40,670 | private static final int getSecurityFlags ( final Map properties ) { int securityType = 0 ; securityType = "true" . equals ( properties . get ( IHtmlToPdfTransformer . PDF_ALLOW_PRINTING ) ) ? ( securityType | PdfWriter . ALLOW_PRINTING ) : securityType ; securityType = "true" . equals ( properties . get ( IHtmlToPdfTr... | return the itext security flags for encryption |
40,671 | public static void destroy ( ) { try { countMutex . acquire ( ) ; for ( int i = 0 ; i < fileToDeleteOnDestroy . size ( ) ; i ++ ) { File f = ( File ) fileToDeleteOnDestroy . get ( i ) ; if ( f != null && f . exists ( ) ) try { f . delete ( ) ; } catch ( Exception ignore ) { } } CClassLoader . destroy ( ) ; } finally { ... | Delete the jar file from the temp directory Destroy the classloader |
40,672 | public final void convertToPdf ( final URL url , final IHtmlToPdfTransformer . PageSize size , final List hf , final OutputStream out , final Map fproperties ) throws CConvertException { Map properties = ( fproperties != null ) ? fproperties : new HashMap ( ) ; ClassLoader loader = Thread . currentThread ( ) . getConte... | Convert the document pointed by url in a PDF file . This method is thread safe . |
40,673 | public final void convertToPdf ( final String content , final IHtmlToPdfTransformer . PageSize size , final List hf , final String furlForBase , final OutputStream out , final Map fproperties ) throws CConvertException { String urlForBase = furlForBase ; Map properties = ( fproperties != null ) ? fproperties : new Hash... | Convert the document in content in a PDF file . This method is thread safe . |
40,674 | private final void init ( boolean useClassLoader ) { final CYaHPConverter converter = this ; System . out . println ( "Initializing..." ) ; long time = System . currentTimeMillis ( ) ; if ( ! useClassLoader ) { System . out . println ( "init time: " + ( System . currentTimeMillis ( ) - time ) ) ; return ; } if ( CClass... | initialize the classloader and the transformer |
40,675 | private IHtmlToPdfTransformer getTransformer ( final Map properties ) { try { mutex . acquire ( ) ; IHtmlToPdfTransformer transformer = null ; String rendererClassName = IHtmlToPdfTransformer . DEFAULT_PDF_RENDERER ; if ( ( properties != null ) && properties . containsKey ( IHtmlToPdfTransformer . PDF_RENDERER_CLASS ) ... | Get a transformer . |
40,676 | protected String signRSAWithQuote ( final List < StringPair > p ) { String param = join ( p , false , true ) ; String sign = rsaSign ( param ) ; return sign ; } | Mobile SDK join the fields with quote which is not documented at all . |
40,677 | public Map < String , Object > calculateObjects ( Map < String , Object > objects ) { Map < String , Object > result = new HashMap < String , Object > ( ) ; return result ; } | this is not the best way |
40,678 | private List < String > existingRootFiles ( ) { List < String > filesFound = new ArrayList < > ( ) ; for ( String path : SU_PATHS ) { if ( new File ( path ) . exists ( ) ) { filesFound . add ( path ) ; } } return filesFound ; } | Checks for files that are known to indicate root . |
40,679 | private List < String > existingRootPackages ( ) { ArrayList < String > packages = new ArrayList < > ( ) ; packages . addAll ( Arrays . asList ( KNOWN_ROOT_APPS_PACKAGES ) ) ; packages . addAll ( Arrays . asList ( KNOWN_DANGEROUS_APPS_PACKAGES ) ) ; packages . addAll ( Arrays . asList ( KNOWN_ROOT_CLOAKING_PACKAGES ) )... | Checks for packages that are known to indicate root . |
40,680 | private List < String > existingDangerousProperties ( ) { String [ ] lines = propertiesReader ( ) ; List < String > propertiesFound = new ArrayList < > ( ) ; for ( String line : lines ) { for ( String key : DANGEROUS_PROPERTIES . keySet ( ) ) { if ( line . contains ( key ) && line . contains ( DANGEROUS_PROPERTIES . ge... | Checks system properties for any dangerous properties that indicate root . |
40,681 | private List < String > existingRWPaths ( ) { String [ ] lines = mountReader ( ) ; List < String > pathsFound = new ArrayList < > ( ) ; for ( String line : lines ) { String [ ] args = line . split ( " " ) ; if ( args . length < 4 ) { Log . e ( TAG , String . format ( "Error formatting mount: %s" , line ) ) ; continue ;... | When you re root you can change the write permissions on common system directories . This method checks if any of the paths in PATHS_THAT_SHOULD_NOT_BE_WRITABLE are writable . |
40,682 | private Request makeRequest ( List < MobileEventJson > batch ) throws IOException { if ( batch . isEmpty ( ) ) { return null ; } Sift . Config config = configProvider . getConfig ( ) ; if ( config == null ) { Log . d ( TAG , "Missing Sift.Config object" ) ; return null ; } if ( config . accountId == null || config . be... | Builds a Request for the specified event batch |
40,683 | public List < T > getList ( ) { if ( isCacheEnabled ) { if ( cachedResult == null ) { cachedResult = makeUnmodifiableUniqueList ( ) ; } return cachedResult ; } else { return makeUnmodifiableUniqueList ( ) ; } } | Returns the list that this ListHolder backs . |
40,684 | private List < T > makeUnmodifiableUniqueList ( ) { Set < T > tmp = newHashSet ( ) ; List < T > uniques = newArrayList ( ) ; for ( T t : getIterable ( ) ) { if ( tmp . add ( t ) ) { uniques . add ( t ) ; } } sort ( uniques ) ; return unmodifiableList ( uniques ) ; } | remove duplication if any |
40,685 | public List < T > getSubList ( int maxSubListSize ) { List < T > subList = newArrayList ( ) ; int counter = 0 ; for ( T t : getList ( ) ) { if ( counter ++ < maxSubListSize ) { subList . add ( t ) ; } else { break ; } } return subList ; } | Returns at most the first maxSubListSize elements of this list . |
40,686 | public SimpleListHolder < T > except ( String ... namesToExclude ) { String key = "current" + getCacheKey ( namesToExclude ) ; SimpleListHolder < T > result = cache . get ( key ) ; if ( result == null ) { result = new SimpleListHolder < T > ( getIterable ( ) , asNameNotEqualsToPredicates ( namesToExclude ) , getSortPro... | Fork this list with extra predicates . |
40,687 | public int inputStreamToOutputStream ( InputStream is , OutputStream os ) throws IOException { byte buffer [ ] = new byte [ 1024 * 100 ] ; int len = - 1 ; int total = 0 ; while ( ( len = is . read ( buffer ) ) >= 0 ) { os . write ( buffer , 0 , len ) ; total += len ; } return total ; } | Write to the outputstream the bytes read from the input stream . |
40,688 | public void inputStreamToFile ( InputStream is , String filename ) throws IOException { FileOutputStream fos = new FileOutputStream ( filename ) ; inputStreamToOutputStream ( is , fos ) ; fos . close ( ) ; } | Write to a file the bytes read from an input stream . |
40,689 | public String inputStreamToString ( InputStream is , String charset ) throws IOException { InputStreamReader isr = null ; if ( null == charset ) { isr = new InputStreamReader ( is ) ; } else { isr = new InputStreamReader ( is , charset ) ; } StringWriter sw = new StringWriter ( ) ; int c = - 1 ; while ( ( c = isr . rea... | Write to a string the bytes read from an input stream . |
40,690 | public boolean isParentAnEmptyDirectory ( File file ) { File parent = file . getParentFile ( ) ; if ( parent != null && parent . exists ( ) && parent . isDirectory ( ) && parent . list ( ) . length == 0 ) { return true ; } return false ; } | Determine if the directory where the passed file resides is empty . |
40,691 | public void pruneEmptyDirs ( File targetFile ) { while ( isParentAnEmptyDirectory ( targetFile ) ) { try { targetFile . getParentFile ( ) . delete ( ) ; targetFile = targetFile . getParentFile ( ) ; } catch ( Exception e ) { } } } | prune empty dir |
40,692 | @ SuppressWarnings ( "unchecked" ) public Collection < String > listFolders ( File folder ) { IOFileFilter ioFileFilter = FileFilterUtils . makeSVNAware ( FileFilterUtils . makeCVSAware ( FileFilterUtils . trueFileFilter ( ) ) ) ; Collection < File > files = FileUtils . listFiles ( folder , FileFilterUtils . fileFileFi... | Recurse in the folder to get the list all files and folders of all non svn files |
40,693 | public void forceDelete ( File tempFile ) { try { if ( tempFile != null && tempFile . exists ( ) ) { FileUtils . forceDelete ( tempFile ) ; } } catch ( Throwable t ) { t . printStackTrace ( ) ; } } | force the deletion of a file |
40,694 | public List < String > getAnnotations ( ) { AnnotationBuilder result = new AnnotationBuilder ( ) ; result . add ( getFixedLengthAnnotation ( ) , getLengthAnnotation ( ) , getNotNullAnnotation ( ) , getNotEmptyAnnotation ( ) , getCharPaddingAnnotation ( ) , getEmailAnnotation ( ) , getDigitsAnnotation ( ) , getSafeHtmlA... | Returns all the validation annotations for the attribute . Imports are processed automatically . |
40,695 | private String convertFileNameToBaseClassName ( String filename ) { if ( filename . endsWith ( "_.java" ) ) { return substringBeforeLast ( filename , "_.java" ) + BASE_SUFFIX_ ; } else { return substringBeforeLast ( filename , ".java" ) + BASE_SUFFIX ; } } | add Base to a given java filename it is used for transparently subclassing generated classes |
40,696 | private String getFullPathForLog ( OutputResult or , String targetFilename ) { if ( or . sameDirectory ( ) ) { return targetFilename ; } else { return or . getGeneratedSource ( ) . getFullPath ( targetFilename ) ; } } | Use it only to display proper path in log |
40,697 | private void buildSimpleEntity ( EntityConfig entityConfig , Entity entity ) { Table table = entity . getTable ( ) ; for ( Column column : table . getColumns ( ) ) { boolean processed = processColumnUsingColumnConfigIfAny ( entityConfig , entity , column ) ; if ( ! processed ) { entity . addAttribute ( attributeFactory... | Build simple entity using user configuration |
40,698 | private void namerDefault ( Entity entity ) { entity . put ( "searchForm" , new ClassNamer2 ( entity , null , "web.domain" , null , "SearchForm" ) ) ; entity . put ( "editForm" , new ClassNamer2 ( entity , null , "web.domain" , null , "EditForm" ) ) ; entity . put ( "graphLoader" , new ClassNamer2 ( entity , null , "we... | Namers declared here can be overridden easily through configuration . |
40,699 | public static String toReadablePluralLabel ( String value ) { String label = toReadableLabel ( value ) ; return label . endsWith ( "ss" ) ? label . substring ( 0 , label . length ( ) - 1 ) : label ; } | Convert strings such as banquePayss to Banque Pays it will remove trailing ss and replace them with s |
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