idx int64 0 165k | question stringlengths 73 5.81k | target stringlengths 5 918 |
|---|---|---|
131,700 | private boolean isMatchingFileExtension ( ) { String [ ] fileExtensions = mediaArgs . getFileExtensions ( ) ; if ( fileExtensions == null || fileExtensions . length == 0 ) { return true ; } for ( String fileExtension : fileExtensions ) { if ( StringUtils . equalsIgnoreCase ( fileExtension , getFileExtension ( ) ) ) { r... | Checks if the file extension of the current binary matches with the requested extensions from the media args . |
131,701 | private Dimension getRequestedDimension ( ) { if ( mediaArgs . getFixedWidth ( ) > 0 || mediaArgs . getFixedHeight ( ) > 0 ) { return new Dimension ( mediaArgs . getFixedWidth ( ) , mediaArgs . getFixedHeight ( ) ) ; } MediaFormat [ ] mediaFormats = mediaArgs . getMediaFormats ( ) ; if ( mediaFormats != null && mediaFo... | Requested dimensions either from media format or fixed dimensions from media args . |
131,702 | public List < Resource > getResources ( ) { return getResources ( ( Predicate < Resource > ) null , ( Resource ) null ) ; } | Get the resources within the current page selected in the suffix of the URL |
131,703 | public String build ( ) { SortedMap < String , Object > sortedParameterMap = new TreeMap < > ( parameterMap ) ; SortedSet < String > resourcePathsSet = new TreeSet < > ( ) ; for ( String nextPart : initialSuffixParts ) { if ( nextPart . indexOf ( KEY_VALUE_DELIMITER ) > 0 ) { String key = decodeKey ( nextPart ) ; if ( ... | Build complete suffix . |
131,704 | private void detectIntegratorTemplateModes ( ) { if ( urlHandlerConfig . getIntegratorModes ( ) . isEmpty ( ) ) { return ; } if ( request != null && RequestPath . hasSelector ( request , SELECTOR_INTEGRATORTEMPLATE_SECURE ) ) { integratorTemplateSecureMode = true ; } else if ( request != null && RequestPath . hasSelect... | Detect integrator template modes - check selectors in current url . |
131,705 | public String getIntegratorTemplateSelector ( ) { if ( currentPage != null && urlHandlerConfig . isIntegrator ( currentPage ) ) { if ( isResourceUrlSecure ( currentPage ) ) { return SELECTOR_INTEGRATORTEMPLATE_SECURE ; } else { return SELECTOR_INTEGRATORTEMPLATE ; } } if ( integratorTemplateSecureMode ) { return SELECT... | Returns selector for integrator template mode . In HTTPS mode the secure selector is returned otherwise the default selector . HTTPS mode is active if the current page is an integrator page and has simple mode - HTTPs activated or the secure integrator mode selector is included in the current request . |
131,706 | @ SuppressWarnings ( "null" ) private IntegratorMode getIntegratorMode ( ValueMap properties ) { IntegratorMode mode = null ; Collection < IntegratorMode > integratorModes = urlHandlerConfig . getIntegratorModes ( ) ; String modeString = properties . get ( IntegratorNameConstants . PN_INTEGRATOR_MODE , String . class )... | Read integrator mode from content container . Defaults to first integrator mode defined . |
131,707 | @ SuppressWarnings ( "null" ) private IntegratorProtocol getIntegratorProtocol ( ValueMap properties ) { IntegratorProtocol protocol = IntegratorProtocol . AUTO ; try { String protocolString = properties . get ( IntegratorNameConstants . PN_INTEGRATOR_PROTOCOL , String . class ) ; if ( StringUtils . isNotEmpty ( protoc... | Read integrator protocol from content container . Default to AUTO . |
131,708 | private boolean isResourceUrlSecure ( Page page ) { ValueMap props = getPagePropertiesNullSafe ( page ) ; IntegratorMode mode = getIntegratorMode ( props ) ; if ( mode . isDetectProtocol ( ) ) { IntegratorProtocol integratorProtocol = getIntegratorProtocol ( props ) ; if ( integratorProtocol == IntegratorProtocol . HTT... | Checks whether resource URLs should be rendered in secure mode or not . |
131,709 | private Page getTargetPage ( String targetPath , InternalLinkResolverOptions options ) { if ( StringUtils . isEmpty ( targetPath ) ) { return null ; } String rewrittenPath ; if ( options . isRewritePathToContext ( ) && ! useTargetContext ( options ) ) { rewrittenPath = urlHandler . rewritePathToContext ( SyntheticNavig... | Returns the target page for the given internal content link reference . Checks validity of page . |
131,710 | private boolean useTargetContext ( InternalLinkResolverOptions options ) { if ( options . isUseTargetContext ( ) && ! options . isRewritePathToContext ( ) ) { return true ; } else if ( currentPage != null && Path . isExperienceFragmentPath ( currentPage . getPath ( ) ) ) { return true ; } return false ; } | Checks if target context should be used . |
131,711 | public final T addCssClass ( String value ) { if ( StringUtils . isNotEmpty ( value ) ) { return setCssClass ( StringUtils . isNotEmpty ( getCssClass ( ) ) ? getCssClass ( ) + " " + value : value ) ; } else { return ( T ) this ; } } | Html class attribute . Adds a single space - separated value while preserving existing ones . |
131,712 | public final Map < String , String > getStyles ( ) { Map < String , String > styleMap = new HashMap < String , String > ( ) ; String styleString = getStyleString ( ) ; if ( styleString != null ) { String [ ] styles = StringUtils . split ( styleString , ";" ) ; for ( String styleSubString : styles ) { String [ ] stylePa... | Html style attribute . |
131,713 | public final T setStyle ( String styleAttribute , String styleValue ) { Map < String , String > styleMap = getStyles ( ) ; styleMap . put ( styleAttribute , styleValue ) ; StringBuilder styleString = new StringBuilder ( ) ; for ( Map . Entry style : styleMap . entrySet ( ) ) { styleString . append ( style . getKey ( ) ... | Html style attribute . Sets single style attribute value . |
131,714 | private static String guessHumanReadableRatioString ( double ratio , NumberFormat numberFormat ) { for ( long width = 1 ; width <= 50 ; width ++ ) { double height = width / ratio ; if ( isLong ( height ) ) { return numberFormat . format ( width ) + ":" + numberFormat . format ( height ) ; } } for ( long width = 1 ; wid... | Try to guess a nice human readable ratio string from the given decimal ratio |
131,715 | public Dimension getMinDimension ( ) { long effWithMin = getEffectiveMinWidth ( ) ; long effHeightMin = getEffectiveMinHeight ( ) ; double effRatio = getRatio ( ) ; if ( effWithMin == 0 && effHeightMin > 0 && effRatio > 0 ) { effWithMin = Math . round ( effHeightMin * effRatio ) ; } if ( effWithMin > 0 && effHeightMin ... | Get minimum dimensions for media format . If only with or height is defined the missing dimensions is calculated from the ratio . If no ratio defined either only width or height dimension is returned . If neither width or height are defined null is returned . |
131,716 | private boolean resolveByNames ( MediaArgs mediaArgs ) { if ( mediaArgs . getMediaFormats ( ) != null ) { return true ; } if ( mediaArgs . getMediaFormatNames ( ) == null ) { return true ; } String [ ] mediaFormatNames = mediaArgs . getMediaFormatNames ( ) ; MediaFormat [ ] mediaFormats = new MediaFormat [ mediaFormatN... | Resolve media format names to media formats so all downstream logic has only to handle the resolved media formats . If resolving fails an exception is thrown . |
131,717 | private boolean addResponsiveImageMediaFormats ( MediaArgs mediaArgs ) { Map < String , MediaFormat > additionalMediaFormats = new LinkedHashMap < > ( ) ; if ( ! resolveForImageSizes ( mediaArgs , additionalMediaFormats ) ) { return false ; } if ( ! resolveForResponsivePictureSources ( mediaArgs , additionalMediaFormat... | Add on - the - fly generated media formats if required for responsive image handling via image sizes or picture sources . |
131,718 | private Asset getInlineAsset ( Resource ntResourceResource , Media media , String fileName ) { return new InlineAsset ( ntResourceResource , media , fileName , adaptable ) ; } | Get implementation of inline media item |
131,719 | private String detectFileName ( Resource referencedResource , Resource ntFileResource , Resource ntResourceResource ) { String fileName = null ; if ( ntFileResource != null && ! referencedResource . equals ( ntFileResource ) ) { fileName = referencedResource . getValueMap ( ) . get ( ntFileResource . getName ( ) + "Nam... | Detect filename for inline binary . |
131,720 | private String cleanupFileName ( String fileName ) { String processedFileName = fileName ; if ( StringUtils . contains ( processedFileName , "/" ) ) { processedFileName = StringUtils . substringAfterLast ( processedFileName , "/" ) ; } if ( StringUtils . contains ( processedFileName , "\\" ) ) { processedFileName = Str... | Make sure filename contains no invalid characters or path parts |
131,721 | private boolean isRenditionMatchSizeSameBigger ( MediaFormat mediaFormat , MediaFormat mediaFormatRequested ) { long widthRequested = mediaFormatRequested . getEffectiveMinWidth ( ) ; long heightRequested = mediaFormatRequested . getEffectiveMinHeight ( ) ; long widthMax = mediaFormat . getEffectiveMaxWidth ( ) ; long ... | Checks if the given media format size is same size or bigger than the requested one . |
131,722 | private boolean isRenditionMatchSizeSameSmaller ( MediaFormat mediaFormat , MediaFormat mediaFormatRequested ) { long widthRequested = mediaFormatRequested . getEffectiveMinWidth ( ) ; long heightRequested = mediaFormatRequested . getEffectiveMinHeight ( ) ; long widthMin = mediaFormat . getEffectiveMinWidth ( ) ; long... | Checks if the given media format size is same size or smaller than the requested one . |
131,723 | private boolean isRenditionMatchExtension ( MediaFormat mediaFormat ) { for ( String extension : mediaFormat . getExtensions ( ) ) { if ( FileExtension . isImage ( extension ) ) { return true ; } } return false ; } | Checks if one of the extensions of the given media format are supported for renditions . |
131,724 | private NavigableSet < RenditionMetadata > rotateSourceRenditions ( Set < RenditionMetadata > candidates ) { if ( rotation == null ) { return new TreeSet < > ( candidates ) ; } return candidates . stream ( ) . map ( rendition -> new VirtualTransformedRenditionMetadata ( rendition . getRendition ( ) , rotateMapWidth ( r... | Rotates all source renditions if configured . |
131,725 | private VirtualTransformedRenditionMetadata getCropRendition ( NavigableSet < RenditionMetadata > candidates ) { RenditionMetadata original = getOriginalRendition ( ) ; if ( original == null ) { return null ; } Double scaleFactor = getCropScaleFactor ( ) ; CropDimension scaledCropDimension = new CropDimension ( Math . ... | Searches for the biggest web - enabled rendition that matches the crop dimensions width and height or is bigger . |
131,726 | private double getCropScaleFactor ( ) { RenditionMetadata original = getOriginalRendition ( ) ; RenditionMetadata webEnabled = AutoCropping . getWebRenditionForCropping ( getAsset ( ) ) ; if ( original == null || webEnabled == null || original . getWidth ( ) == 0 || webEnabled . getWidth ( ) == 0 ) { return 1d ; } retu... | The cropping coordinates are stored with coordinates relating to the web - enabled rendition . But we want to crop the original image so we have to scale those values to match the coordinates in the original image . |
131,727 | static Resource get ( String path , ResourceResolver resolver ) { Resource resource = resolver . getResource ( path ) ; if ( resource != null ) { return resource ; } return new SyntheticNavigatableResource ( path , resolver ) ; } | Get resource for path . If the path does not exist a synthetic resource is created which supports navigation over it s parents until it reaches a resource that exists . |
131,728 | public MediaArgs dragDropSupport ( DragDropSupport value ) { if ( value == null ) { throw new IllegalArgumentException ( "No null value allowed for drag&drop support." ) ; } this . dragDropSupport = value ; return this ; } | Drag& ; Drop support for media builder . |
131,729 | public static String getImageFileName ( String originalFilename ) { String namePart = StringUtils . substringBeforeLast ( originalFilename , "." ) ; String extensionPart = StringUtils . substringAfterLast ( originalFilename , "." ) ; if ( StringUtils . equalsIgnoreCase ( extensionPart , FileExtension . PNG ) ) { extens... | Get image filename to be used for the URL with file extension matching the image format which is produced by this servlet . |
131,730 | public static String toHtml5DataName ( String headlessCamelCaseName ) { if ( StringUtils . isEmpty ( headlessCamelCaseName ) ) { throw new IllegalArgumentException ( "Property name is empty." ) ; } if ( ! isHeadlessCamelCaseName ( headlessCamelCaseName ) ) { throw new IllegalArgumentException ( "This is not a valid hea... | Converts a headless camel case property name to a HTML5 data attribute name including data - prefix . |
131,731 | public static String toHeadlessCamelCaseName ( String html5DataName ) { if ( StringUtils . isEmpty ( html5DataName ) ) { throw new IllegalArgumentException ( "Property name is empty." ) ; } if ( ! isHtml5DataName ( html5DataName ) ) { throw new IllegalArgumentException ( "This is not a valid HTML5 data property name: "... | Converts a HTML5 data attribute name including data - prefix to a headless camel case name . |
131,732 | public final org . jdom2 . Element setName ( String value ) { return super . setName ( value ) ; } | Sets element name - should not be used for HtmlElement - derived classes! |
131,733 | public final int getAttributeValueAsInteger ( String attributeName ) { Attribute attribute = getAttribute ( attributeName ) ; if ( attribute == null ) { return 0 ; } else { try { return attribute . getIntValue ( ) ; } catch ( DataConversionException ex ) { return 0 ; } } } | Gets attribute value as integer . |
131,734 | public final T setAttributeValueAsLong ( String name , long value ) { setAttribute ( name , Long . toString ( value ) ) ; return ( T ) this ; } | Sets attribute value as long . |
131,735 | public final long getAttributeValueAsLong ( String attributeName ) { Attribute attribute = getAttribute ( attributeName ) ; if ( attribute == null ) { return 0 ; } else { try { return attribute . getLongValue ( ) ; } catch ( DataConversionException ex ) { return 0 ; } } } | Gets attribute value as long . |
131,736 | public final T setAttributeValueAsInteger ( String name , int value ) { setAttribute ( name , Integer . toString ( value ) ) ; return ( T ) this ; } | Sets attribute value as integer . |
131,737 | public final org . jdom2 . Element addContent ( Content content ) { if ( content == null ) { return null ; } return super . addContent ( content ) ; } | Appends the child to the end of the element s content list |
131,738 | public final org . jdom2 . Element addContent ( Collection collection ) { if ( collection == null ) { return null ; } return super . addContent ( collection ) ; } | Appends all children in the given collection to the end of the content list . In event of an exception during add the original content will be unchanged and the objects in the supplied collection will be unaltered . |
131,739 | public InputSource resolveEntity ( String publicId , String systemId ) throws SAXException , IOException { String filename = xhtmlResourceMap . get ( publicId ) ; if ( filename != null ) { String resourceName = resourceFolder + "/" + filename ; InputStream is = XHtmlEntityResolver . class . getResourceAsStream ( resour... | Resolve XHtml resource entities load from classpath resources . |
131,740 | Object readResolve ( ) { if ( favorites != null ) { data = Maps . newConcurrentMap ( ) ; for ( String job : favorites ) { data . put ( job , true ) ; } favorites = null ; } return this ; } | Migrates this properties storage from favourite s list to a map of booleans |
131,741 | public ICommonsList < IIndexerWorkItem > stop ( ) { m_aImmediateCollector . stopQueuingNewObjects ( ) ; final ICommonsList < IIndexerWorkItem > aRemainingItems = m_aImmediateCollector . drainQueue ( ) ; ExecutorServiceHelper . shutdownAndWaitUntilAllTasksAreFinished ( m_aSenderThreadPool ) ; return aRemainingItems ; } | Stop the indexer work queue immediately . |
131,742 | public void queueObject ( final IIndexerWorkItem aItem ) { ValueEnforcer . notNull ( aItem , "Item" ) ; m_aImmediateCollector . queueObject ( aItem ) ; } | Queue a work item and handle it asynchronously . |
131,743 | public void addItem ( final ReIndexWorkItem aItem ) throws IllegalStateException { ValueEnforcer . notNull ( aItem , "Item" ) ; m_aRWLock . writeLocked ( ( ) -> { internalCreateItem ( aItem ) ; } ) ; LOGGER . info ( "Added " + aItem . getLogText ( ) + " to re-try list for retry #" + ( aItem . getRetryCount ( ) + 1 ) ) ... | Add a unique item to the list . |
131,744 | private EChange _queueUniqueWorkItem ( final IIndexerWorkItem aWorkItem ) { ValueEnforcer . notNull ( aWorkItem , "WorkItem" ) ; m_aRWLock . writeLock ( ) . lock ( ) ; try { if ( ! m_aUniqueItems . add ( aWorkItem ) ) { LOGGER . info ( "Ignoring work item " + aWorkItem . getLogText ( ) + " because it is already in the ... | Queue a single work item of any type . If the item is already in the queue it is ignored . |
131,745 | public EChange queueWorkItem ( final IParticipantIdentifier aParticipantID , final EIndexerWorkItemType eType , final String sOwnerID , final String sRequestingHost ) { final IIndexerWorkItem aWorkItem = new IndexerWorkItem ( aParticipantID , eType , sOwnerID , sRequestingHost ) ; return _queueUniqueWorkItem ( aWorkIte... | Queue a new work item |
131,746 | public void expireOldEntries ( ) { final ICommonsList < IReIndexWorkItem > aExpiredItems = m_aReIndexList . getAndRemoveAllEntries ( IReIndexWorkItem :: isExpired ) ; if ( aExpiredItems . isNotEmpty ( ) ) { LOGGER . info ( "Expiring " + aExpiredItems . size ( ) + " re-index work items and move them to the dead list" ) ... | Expire all re - index entries that are in the list for a too long time . This is called from a scheduled job only . All respective items are move from the re - index list to the dead list . |
131,747 | public void reIndexParticipantData ( ) { final LocalDateTime aNow = PDTFactory . getCurrentLocalDateTime ( ) ; final List < IReIndexWorkItem > aReIndexNowItems = m_aReIndexList . getAndRemoveAllEntries ( aWorkItem -> aWorkItem . isRetryPossible ( aNow ) ) ; if ( LOGGER . isDebugEnabled ( ) ) LOGGER . debug ( "Re-indexi... | Re - index all entries that are ready to be re - indexed now . This is called from a scheduled job only . |
131,748 | public static ClientCertificateValidationResult verifyClientCertificate ( final HttpServletRequest aHttpRequest , final String sLogPrefix ) { if ( s_bIsCheckDisabled . get ( ) ) { if ( LOGGER . isDebugEnabled ( ) ) LOGGER . debug ( sLogPrefix + "Client certificate is considered valid because the 'allow all' for tests i... | Extract certificates from request and validate them . |
131,749 | public static IMultiMapListBased < IParticipantIdentifier , PDStoredBusinessEntity > getGroupedByParticipantID ( final Iterable < PDStoredBusinessEntity > aDocs ) { final MultiLinkedHashMapArrayListBased < IParticipantIdentifier , PDStoredBusinessEntity > ret = new MultiLinkedHashMapArrayListBased < > ( ) ; for ( final... | Group the passed document list by participant ID |
131,750 | private static ClientCertificateValidationResult _checkClientCertificate ( final HttpServletRequest aHttpServletRequest , final String sLogPrefix ) { try { return ClientCertificateValidator . verifyClientCertificate ( aHttpServletRequest , sLogPrefix ) ; } catch ( final RuntimeException ex ) { if ( LOGGER . isWarnEnabl... | Check if the current request contains a client certificate and whether it is valid . |
131,751 | public void incRetryCount ( ) { m_nRetries ++ ; m_aPreviousRetryDT = PDTFactory . getCurrentLocalDateTime ( ) ; m_aNextRetryDT = m_aPreviousRetryDT . plusMinutes ( PDServerConfiguration . getReIndexRetryMinutes ( ) ) ; } | Increment the number of retries and update the previous and the next retry datetime . |
131,752 | public IndexSearcher getSearcher ( ) throws IOException { _checkClosing ( ) ; final IndexReader aReader = getReader ( ) ; if ( aReader == null ) { LOGGER . warn ( "Index not readable" ) ; return null ; } if ( m_aSearchReader == aReader ) { assert m_aSearcher != null ; } else { m_aSearchReader = aReader ; m_aSearcher = ... | Get a searcher on this index . |
131,753 | @ MustBeLocked ( ELockType . WRITE ) public void updateDocuments ( final Term aDelTerm , final Iterable < ? extends Iterable < ? extends IndexableField > > aDocs ) throws IOException { long nSeqNum ; if ( false ) { nSeqNum = _getWriter ( ) . deleteDocuments ( aDelTerm ) ; nSeqNum = _getWriter ( ) . updateDocuments ( nu... | Atomically deletes documents matching the provided delTerm and adds a block of documents with sequentially assigned document IDs such that an external reader will see all or none of the documents . |
131,754 | public ESuccess writeLockedAtomic ( final IThrowingRunnable < IOException > aRunnable ) throws IOException { m_aRWLock . writeLock ( ) . lock ( ) ; try { if ( isClosing ( ) ) { LOGGER . info ( "Cannot executed something write locked, because Lucene is shutting down" ) ; return ESuccess . FAILURE ; } aRunnable . run ( )... | Run the provided action within a locked section . |
131,755 | public final NATIVE_TYPE getDocValue ( final Document aDoc ) { final IndexableField aField = getDocField ( aDoc ) ; if ( aField != null ) return getFieldNativeValue ( aField ) ; return null ; } | Get the value of this field in the provided document |
131,756 | public static PDBusinessCard parseBusinessCard ( final byte [ ] aData , final Charset aCharset ) { ValueEnforcer . notNull ( aData , "Data" ) ; { final PD1BusinessCardMarshaller aMarshaller1 = new PD1BusinessCardMarshaller ( ) ; aMarshaller1 . readExceptionCallbacks ( ) . removeAll ( ) ; if ( aCharset != null ) aMarsha... | A generic reading API to read all supported versions of the BusinessCard from a byte array and an optional character set . |
131,757 | public static PDBusinessCard parseBusinessCard ( final Node aNode ) { ValueEnforcer . notNull ( aNode , "Node" ) ; { final PD1BusinessCardMarshaller aMarshaller1 = new PD1BusinessCardMarshaller ( ) ; aMarshaller1 . readExceptionCallbacks ( ) . removeAll ( ) ; final PD1BusinessCardType aBC1 = aMarshaller1 . read ( aNode... | A generic reading API to read all supported versions of the BusinessCard from a DOM node . |
131,758 | public static ClientCertificateValidationResult createSuccess ( final String sClientID ) { ValueEnforcer . notEmpty ( sClientID , "ClientID" ) ; return new ClientCertificateValidationResult ( true , sClientID ) ; } | Create client certificate validation success |
131,759 | protected < T > T executeRequest ( final HttpRequestBase aRequest , final ResponseHandler < T > aHandler ) throws IOException { final HttpContext aContext = HttpClientHelper . createHttpContext ( m_aProxy , m_aProxyCredentials ) ; return m_aHttpClientMgr . execute ( aRequest , aContext , aHandler ) ; } | The main execution routine . Overwrite this method to add additional properties to the call . |
131,760 | public boolean isServiceGroupRegistered ( final IParticipantIdentifier aParticipantID ) { ValueEnforcer . notNull ( aParticipantID , "ParticipantID" ) ; final HttpGet aGet = new HttpGet ( m_sPDIndexerURL + aParticipantID . getURIPercentEncoded ( ) ) ; try { return executeRequest ( aGet , new PDClientResponseHandler ( )... | Gets a list of references to the CompleteServiceGroup s owned by the specified userId . This is a non - specification compliant method . |
131,761 | public static void streamFileXMLTo ( final UnifiedResponse aUR ) { s_aRWLock . readLock ( ) . lock ( ) ; try { final File f = _getFileXML ( ) ; aUR . setContent ( new FileSystemResource ( f ) ) ; } finally { s_aRWLock . readLock ( ) . unlock ( ) ; } } | Stream the stored XML file to the provided HTTP response |
131,762 | public static void streamFileExcelTo ( final UnifiedResponse aUR ) { s_aRWLock . readLock ( ) . lock ( ) ; try { final File f = _getFileExcel ( ) ; aUR . setContent ( new FileSystemResource ( f ) ) ; } finally { s_aRWLock . readLock ( ) . unlock ( ) ; } } | Stream the stored Excel file to the provided HTTP response |
131,763 | public static ESuccess executeWorkItem ( final IPDStorageManager aStorageMgr , final IIndexerWorkItem aWorkItem , final int nRetryCount , final Consumer < ? super IIndexerWorkItem > aSuccessHandler , final Consumer < ? super IIndexerWorkItem > aFailureHandler ) { LOGGER . info ( "Execute work item " + aWorkItem . getLo... | This method is responsible for executing the specified work item depending on its type . |
131,764 | protected BufferedInputStream buffer ( final InputStream inputStream ) { if ( inputStream == null ) { throw new NullPointerException ( "inputStream == null" ) ; } return inputStream instanceof BufferedInputStream ? ( BufferedInputStream ) inputStream : new BufferedInputStream ( inputStream ) ; } | stolen from commons - io IOUtiles ( |
131,765 | public int exitValue ( ) throws ManagedProcessException { try { return resultHandler . getExitValue ( ) ; } catch ( IllegalStateException e ) { throw new ManagedProcessException ( "Exit Value not (yet) available for " + getProcLongName ( ) , e ) ; } } | Returns the exit value for the subprocess . |
131,766 | public void close ( ) { if ( ! closed . compareAndSet ( false , true ) ) return ; try { synchronized ( inputStream ) { inputStream . close ( ) ; } } catch ( IOException ex ) { throw new RuntimeException ( ex ) ; } } | Closes the output port |
131,767 | public void write ( OutputStream stream ) throws IOException { ByteArrayOutputStream bos = new ByteArrayOutputStream ( ) ; DeflaterOutputStream deflate = new DeflaterOutputStream ( bos ) ; DataOutputStream dataStream = new DataOutputStream ( deflate ) ; dataStream . writeLong ( step ) ; dataStream . writeLong ( getStar... | Writes this index to specified output stream . |
131,768 | public static FileIndex read ( InputStream stream ) throws IOException { DataInputStream raw = new DataInputStream ( stream ) ; int magic = raw . readInt ( ) ; if ( magic != MAGIC ) throw new IOException ( "Wrong magic number" ) ; int length = raw . readInt ( ) ; byte [ ] buffer = new byte [ length ] ; raw . read ( buf... | Reads index from input stream . |
131,769 | public static void register ( Alphabet alphabet ) { if ( alphabetsByName . put ( alphabet . getAlphabetName ( ) , alphabet ) != null ) throw new IllegalStateException ( "Alphabet with this name is already registered." ) ; if ( alphabetsById . put ( alphabet . getId ( ) , alphabet ) != null ) throw new IllegalStateExcep... | Register new alphabet |
131,770 | public static < T > OutputPortCloseable < T > sort ( OutputPort < T > initialSource , Comparator < T > comparator , int chunkSize , Class < T > clazz , File tempFile ) throws IOException { return sort ( initialSource , comparator , chunkSize , new ObjectSerializer . PrimitivIOObjectSerializer < > ( clazz ) , tempFile )... | Sort objects supporting PrimitivIO serialization . |
131,771 | private void move1 ( ) { if ( node == null ) return ; if ( position >= reference . size ( ) ) { node = null ; return ; } node = node . links [ reference . codeAt ( position ++ ) ] ; } | Move the pointer one step forward . Move is made exactly matching the corresponding nucleotide in the reference sequence so this method prevents branching in the current position . |
131,772 | public void seekToRecord ( long recordNumber ) throws IOException { if ( currentRecordNumber == recordNumber ) return ; long skip ; if ( recordNumber < fileIndex . getStartingRecordNumber ( ) ) { if ( currentRecordNumber < recordNumber ) skip = recordNumber - currentRecordNumber ; else { skip = recordNumber ; seek0 ( 0... | Sets the file - pointer offset measured from the beginning of this file at which the next record occurs . |
131,773 | public T take ( ) { T t = take0 ( ) ; if ( t != null ) ++ currentRecordNumber ; return t ; } | Returns the next record or null if no more records exist . |
131,774 | public int getLengthDelta ( ) { int delta = 0 ; for ( int mut : mutations ) switch ( mut & MUTATION_TYPE_MASK ) { case RAW_MUTATION_TYPE_DELETION : -- delta ; break ; case RAW_MUTATION_TYPE_INSERTION : ++ delta ; break ; } return delta ; } | Returns the difference between the length of initial sequence and length of mutated sequence . Negative values denotes that mutated sequence is shorter . |
131,775 | public Mutations < S > concat ( final Mutations < S > other ) { return new MutationsBuilder < > ( alphabet , false ) . ensureCapacity ( this . size ( ) + other . size ( ) ) . append ( this ) . append ( other ) . createAndDestroy ( ) ; } | Concatenates this and other |
131,776 | public Mutations < S > move ( int offset ) { int [ ] newMutations = new int [ mutations . length ] ; for ( int i = 0 ; i < mutations . length ; ++ i ) newMutations [ i ] = Mutation . move ( mutations [ i ] , offset ) ; return new Mutations < S > ( alphabet , newMutations , true ) ; } | Moves positions of mutations by specified offset |
131,777 | public Mutations < S > removeMutationsInRange ( int from , int to ) { if ( to < from ) throw new IllegalArgumentException ( "Reversed ranges are not supported." ) ; if ( from == to ) return this ; long indexRange = getIndexRange ( from , to ) ; int fromIndex = ( int ) ( indexRange >>> 32 ) , toIndex = ( int ) ( indexRa... | Removes mutations for a range of positions in the original sequence and performs shift of corresponding positions of mutations . |
131,778 | public static long [ ] getSortedDistinct ( long [ ] values ) { if ( values . length == 0 ) return values ; Arrays . sort ( values ) ; int shift = 0 ; int i = 0 ; while ( i + shift + 1 < values . length ) if ( values [ i + shift ] == values [ i + shift + 1 ] ) ++ shift ; else { values [ i ] = values [ i + shift ] ; ++ i... | Sort array & return array with removed repetitive values . |
131,779 | public String toPrettyString ( ) { String seq = sequence . toString ( ) ; String qual = quality . toString ( ) ; return seq + '\n' + qual ; } | Returns a pretty string representation of this . |
131,780 | private void ensureCapacity ( int newSize ) { int oldSize ; if ( ( oldSize = branchingEnumerators . length ) < newSize ) { branchingEnumerators = Arrays . copyOfRange ( branchingEnumerators , 0 , newSize ) ; for ( int i = oldSize ; i < newSize ; ++ i ) branchingEnumerators [ i ] = new BranchingEnumerator < > ( referenc... | Ensures capacity for storing BranchingEnumerators . |
131,781 | private void setupBranchingEnumerators ( ) { final byte [ ] bSequence = branchingSequences [ branchingSequenceIndex ] ; ensureCapacity ( bSequence . length ) ; byte previous = - 1 , current ; for ( int i = 0 ; i < bSequence . length ; ++ i ) { current = bSequence [ i ] ; boolean autoMove1 = ( previous == 1 && current =... | Setts up BranchingEnumerators for current branching sequence |
131,782 | public static LinearGapAlignmentScoring < AminoAcidSequence > getAminoAcidBLASTScoring ( BLASTMatrix matrix , int gapPenalty ) { return new LinearGapAlignmentScoring < > ( AminoAcidSequence . ALPHABET , matrix . getMatrix ( ) , gapPenalty ) ; } | Returns standard amino acid BLAST scoring |
131,783 | public static RandomAccessFastaIndex index ( Path file , int indexStep , boolean save , LongProcessReporter reporter ) { Path indexFile = file . resolveSibling ( file . getFileName ( ) + INDEX_SUFFIX ) ; if ( Files . exists ( indexFile ) ) try ( FileInputStream fis = new FileInputStream ( indexFile . toFile ( ) ) ) { R... | Index fasta file or loads previously created index |
131,784 | public static KAlignerParameters getByName ( String name ) { KAlignerParameters params = knownParameters . get ( name ) ; if ( params == null ) return null ; return params . clone ( ) ; } | Returns parameters by specified preset name |
131,785 | public OutputPortCloseable < RawFastaRecord > asRawRecordsPort ( ) { return new OutputPortCloseable < RawFastaRecord > ( ) { public void close ( ) { FastaReader . this . close ( ) ; } public RawFastaRecord take ( ) { return takeRawRecord ( ) ; } } ; } | Returns output port of raw records . |
131,786 | public static SourceInformation from ( Pattern sourceRegex , String name ) { if ( sourceRegex == null ) { return new SourceInformation ( null , name ) ; } Matcher matcher = sourceRegex . matcher ( name ) ; if ( matcher . groupCount ( ) != 1 ) { log . error ( "Source regex matcher must define a group" ) ; return new Sou... | If the pattern is not null it will attempt to match against the supplied name to pull out the source . |
131,787 | public static < T , S extends Sequence < S > > List < Cluster < T > > performClustering ( Collection < T > inputObjects , SequenceExtractor < T , S > sequenceExtractor , ClusteringStrategy < T , S > strategy ) { return new Clustering < > ( inputObjects , sequenceExtractor , strategy ) . performClustering ( ) ; } | Helper method . See class description . |
131,788 | public int calculateScore ( AlignmentScoring < S > scoring ) { return AlignmentUtils . calculateScore ( sequence1 , sequence1Range , mutations , scoring ) ; } | Calculates score for this alignment using another scoring . |
131,789 | public Range convertToSeq1Range ( Range rangeInSeq2 ) { int from = aabs ( convertToSeq1Position ( rangeInSeq2 . getFrom ( ) ) ) ; int to = aabs ( convertToSeq1Position ( rangeInSeq2 . getTo ( ) ) ) ; if ( from == - 1 || to == - 1 ) return null ; return new Range ( from , to ) ; } | Converts range in sequence2 to range in sequence1 or returns null if input range is not fully covered by alignment |
131,790 | public Range convertToSeq2Range ( Range rangeInSeq1 ) { int from = aabs ( convertToSeq2Position ( rangeInSeq1 . getFrom ( ) ) ) ; int to = aabs ( convertToSeq2Position ( rangeInSeq1 . getTo ( ) ) ) ; if ( from == - 1 || to == - 1 ) return null ; return new Range ( from , to ) ; } | Converts range in sequence1 to range in sequence2 or returns null if input range is not fully covered by alignment |
131,791 | public Alignment < S > invert ( S sequence2 ) { return new Alignment < > ( sequence2 , getRelativeMutations ( ) . invert ( ) . move ( sequence2Range . getFrom ( ) ) , sequence2Range , sequence1Range , score ) ; } | Having sequence2 creates alignment from sequence2 to sequence1 |
131,792 | public float similarity ( ) { int match = 0 , mismatch = 0 ; AlignmentIteratorForward < S > iterator = forwardIterator ( ) ; while ( iterator . advance ( ) ) { final int mut = iterator . getCurrentMutation ( ) ; if ( mut == NON_MUTATION ) ++ match ; else ++ mismatch ; } return 1.0f * match / ( match + mismatch ) ; } | Returns number of matches divided by sum of number of matches and mismatches . |
131,793 | public Long peekDelta ( String name , long count ) { Long previous = lookup . get ( name ) ; return calculateDelta ( name , previous , count ) ; } | Gets the delta without updating the internal data store |
131,794 | public Long getDelta ( String name , long count ) { Long previous = lookup . put ( name , count ) ; return calculateDelta ( name , previous , count ) ; } | Calculates the delta . If this is a new value that has not been seen before zero will be assumed to be the initial value . Updates the internal map with the supplied count . |
131,795 | public static Range extendRange ( SequenceQuality quality , QualityTrimmerParameters parameters , Range initialRange ) { int lower = pabs ( trim ( quality , 0 , initialRange . getLower ( ) , - 1 , false , parameters ) ) ; int upper = pabs ( trim ( quality , initialRange . getUpper ( ) , quality . size ( ) , + 1 , false... | Extend initialRange to the biggest possible range that fulfils the criteria of QualityTrimmer along the whole extended region . |
131,796 | public static Range trim ( SequenceQuality quality , QualityTrimmerParameters parameters ) { return trim ( quality , parameters , new Range ( 0 , quality . size ( ) ) ) ; } | Trims the quality string by cutting off low quality nucleotides on both edges . |
131,797 | public static Range trim ( SequenceQuality quality , QualityTrimmerParameters parameters , Range initialRange ) { int lower = pabs ( trim ( quality , initialRange . getLower ( ) , initialRange . getUpper ( ) , + 1 , true , parameters ) ) + 1 ; assert lower >= initialRange . getLower ( ) ; if ( lower == initialRange . g... | Trims the initialRange by cutting off low quality nucleotides on both edges . |
131,798 | public static AminoAcidSequence translate ( NucleotideSequence sequence ) { if ( sequence . size ( ) % 3 != 0 ) throw new IllegalArgumentException ( "Only nucleotide sequences with size multiple " + "of three are supported (in-frame)." ) ; byte [ ] aaData = new byte [ sequence . size ( ) / 3 ] ; GeneticCode . translate... | Translates sequence having length divisible by 3 starting from first nucleotide . |
131,799 | public void validate ( ) { for ( String in : getInputFiles ( ) ) { if ( ! new File ( in ) . exists ( ) ) throwValidationException ( "ERROR: input file \"" + in + "\" does not exist." , false ) ; validateInfo ( in ) ; } } | Validate injected parameters and options |
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