idx int64 0 165k | question stringlengths 73 5.81k | target stringlengths 5 918 |
|---|---|---|
141,700 | public static void dumpBeansNames ( ) { DefaultListableBeanFactory f = ( DefaultListableBeanFactory ) context . getBeanFactory ( ) ; String [ ] beanDefinitionNames = f . getBeanDefinitionNames ( ) ; for ( String name : beanDefinitionNames ) { JK . print ( name , " for class :" , f . getBean ( name ) . getClass ( ) . ge... | Dump beans names . |
141,701 | protected static Configuration getConfig ( String path ) { if ( cfg == null ) { cfg = new Configuration ( ) ; cfg . setClassForTemplateLoading ( TemplateUtil . class , path == null ? "/templates" : path ) ; cfg . setLocale ( Locale . US ) ; cfg . setTemplateExceptionHandler ( TemplateExceptionHandler . RETHROW_HANDLER ... | Gets the config . |
141,702 | protected void handleClient ( final Socket client ) throws IOException { final ClientHandler handler = new ClientHandler ( client ) ; this . executorService . execute ( handler ) ; } | Handle client request this method will be called when new client connection received by the start method . |
141,703 | public synchronized void stop ( ) throws IOException { this . stopped = true ; if ( this . server != null && this . waitingClient ) { this . server . close ( ) ; this . server = null ; } } | Stop the server instance by setting the stopped flag to true the close the server instance if open . |
141,704 | private void resetConfigToDefault ( ) { isUseWebservice = true ; isUpdateAutomatic = true ; isUseExternalMonomers = false ; isUseExternalNucleotides = false ; setUseExternalAttachments ( false ) ; webserviceMonomersURL = "http://localhost:8080/HELM2MonomerService/rest" ; webserviceMonomersPath = "monomer/" ; webservice... | Resets the configuration to default values . |
141,705 | public void refresh ( ) { File configFile = new File ( CONFIG_FILE_PATH ) ; if ( ! configFile . exists ( ) ) { BufferedWriter writer = null ; BufferedReader reader = null ; try { configFile . createNewFile ( ) ; InputStream in = Chemistry . class . getResourceAsStream ( "/org/helm/notation2/resources/MonomerStoreConfig... | Refreshes the configuration using the local properties file . |
141,706 | private static void addEntry ( final ArrayList < String > aStringArray ) { try { final MagicMimeEntry magicEntry = new MagicMimeEntry ( aStringArray ) ; mMagicMimeEntries . add ( magicEntry ) ; } catch ( final InvalidMagicMimeEntryException e ) { } } | Adds the entry . |
141,707 | private static String getMagicMimeType ( final byte [ ] bytes ) throws IOException { final int len = mMagicMimeEntries . size ( ) ; for ( int i = 0 ; i < len ; i ++ ) { final MagicMimeEntry me = mMagicMimeEntries . get ( i ) ; final String mtype = me . getMatch ( bytes ) ; if ( mtype != null ) { return mtype ; } } retu... | Gets the magic mime type . |
141,708 | public static String getMimeType ( final byte [ ] data ) { String mimeType = null ; try { mimeType = MimeUtil . getMagicMimeType ( data ) ; } catch ( final Exception e ) { } finally { if ( mimeType == null ) { mimeType = UNKNOWN_MIME_TYPE ; } } return mimeType ; } | Gets the mime type . |
141,709 | private static void parse ( final Reader r ) throws IOException { final BufferedReader br = new BufferedReader ( r ) ; String line ; final ArrayList < String > sequence = new ArrayList < String > ( ) ; line = br . readLine ( ) ; while ( true ) { if ( line == null ) { break ; } line = line . trim ( ) ; if ( line . lengt... | Parse the magic . mime file |
141,710 | public static JKContext getCurrentContext ( ) { JKContext context = ( JKContext ) JKThreadLocal . getValue ( JKContextConstants . JK_CONTEXT ) ; if ( context == null ) { context = getInstance ( ) . createDesktopContext ( ) ; JKThreadLocal . setValue ( JKContextConstants . JK_CONTEXT , context ) ; } return context ; } | Gets the current context . |
141,711 | public static byte [ ] generateImageHELMMolecule ( HELM2Notation helm2notation ) throws BuilderMoleculeException , CTKException , IOException , ChemistryException { LOG . info ( "Image generation process of HELM molecule starts" ) ; String smiles = SMILES . getSMILESForAll ( helm2notation ) ; LOG . info ( "Get for the ... | method to generate an image of the HELM molecule |
141,712 | public static List < String > getAminoAcidList ( String peptideSequence ) throws MonomerException , NotationException , MonomerLoadingException , ChemistryException { if ( null == peptideSequence ) { throw new NotationException ( "Peptide Sequence must be specified" ) ; } String cleanSeq = cleanup ( peptideSequence ) ;... | This method converts peptide sequence into a List of amino acid |
141,713 | public static List < String > getAminoAcidList ( String peptideSequence , String delimiter ) throws MonomerException , NotationException , MonomerLoadingException , ChemistryException { if ( null == peptideSequence ) { throw new NotationException ( "Peptide Sequence must be specified" ) ; } if ( null == delimiter || de... | This method converts peptide sequence into a List of amino acid with optional delimiter |
141,714 | public static String cleanup ( String sequence ) { String result = sequence . replaceAll ( "\\s" , "" ) ; if ( result . equals ( result . toLowerCase ( ) ) ) { result = result . toUpperCase ( ) ; } return result ; } | remove white space and convert all lower case to upper case |
141,715 | public static void downloadFile ( final String fileUrl , final String localFile ) throws IOException { final URL url = new URL ( fileUrl ) ; final HttpURLConnection connection = ( HttpURLConnection ) url . openConnection ( ) ; final byte [ ] data = JKIOUtil . readStream ( connection . getInputStream ( ) ) ; JKIOUtil . ... | Download file . |
141,716 | public static File downloadFileToTemp ( final String fileUrl , final String ext ) throws IOException { final File file = File . createTempFile ( "jk-" , ext ) ; JKHttpUtil . downloadFile ( fileUrl , file . getAbsolutePath ( ) ) ; return file ; } | Download file to temp . |
141,717 | public static String requestUrl ( final String url , final String method , final Properties header , final String body ) { try { final URL siteUrl = new URL ( url ) ; final HttpURLConnection connection = ( HttpURLConnection ) siteUrl . openConnection ( ) ; connection . setRequestMethod ( method ) ; final Enumeration < ... | Send http request . |
141,718 | public static String getUrlContents ( String urlString ) { HttpURLConnection con = null ; try { URL url = new URL ( urlString ) ; con = ( HttpURLConnection ) url . openConnection ( ) ; con . connect ( ) ; InputStream inputStream = con . getInputStream ( ) ; BufferedReader reader = new BufferedReader ( new InputStreamRe... | Gets the url contents . |
141,719 | public static String getValueFromUrl ( String url , String preText , int length ) { String urlContents = getUrlContents ( url ) ; int indexOf = urlContents . indexOf ( preText ) ; if ( indexOf != - 1 ) { indexOf += preText . length ( ) ; String substring = urlContents . substring ( indexOf , indexOf + length ) ; return... | Gets the value from url based on pre - text value from the response . |
141,720 | public static InputStream getUrlInputStream ( String urlString ) { URL url ; try { url = new URL ( urlString ) ; HttpURLConnection con = ( HttpURLConnection ) url . openConnection ( ) ; con . connect ( ) ; return con . getInputStream ( ) ; } catch ( Exception e ) { throw new JKException ( e ) ; } } | Gets the url input stream . |
141,721 | public static < T > T readUrlAsObject ( String url , Class < T > type ) { String contents = getUrlContents ( url ) ; ObjectMapper mapper = new ObjectMapper ( ) ; mapper . enableDefaultTyping ( ) ; try { return mapper . readValue ( contents , type ) ; } catch ( IOException e ) { JK . throww ( e ) ; return null ; } } | Read the given url contents and try to create an object from the given type . |
141,722 | public static Password createPassword ( char [ ] password ) { byte [ ] salt = JKSecurityUtil . salt ( ) ; byte [ ] hash = JKSecurityUtil . hash ( password , salt ) ; Password pass = new Password ( ) ; pass . setHash ( encodeInToBase64 ( hash ) ) ; pass . setSalt ( encodeInToBase64 ( salt ) ) ; return pass ; } | Encrypt password . |
141,723 | public Class < ? > getJavaType ( ) { if ( javaType == null ) { javaType = JKTypeMapping . getType ( getCode ( ) ) . getClass ( ) ; if ( javaType == null ) { JK . error ( "JKType cannot by null, and code not avaiable %s" , code ) ; } } return javaType ; } | Gets the java type . |
141,724 | public String getName ( ) { if ( name == null ) { name = JKMessage . get ( getJavaType ( ) . getSimpleName ( ) ) ; } return name ; } | Gets the name . |
141,725 | public JKTimeObject toTimeObject ( Date date , Date time ) { JKTimeObject fsTimeObject = new JKTimeObject ( ) ; Calendar timeInstance = Calendar . getInstance ( ) ; timeInstance . setTimeInMillis ( time . getTime ( ) ) ; fsTimeObject . setHour ( timeInstance . get ( Calendar . HOUR_OF_DAY ) ) ; fsTimeObject . setMunite... | To time object . |
141,726 | public static RgroupStructure buildMoleculefromSinglePolymer ( final PolymerNotation polymernotation ) throws BuilderMoleculeException , HELM2HandledException , ChemistryException { LOG . info ( "Build molecule for single Polymer " + polymernotation . getPolymerID ( ) . getId ( ) ) ; if ( polymernotation . getPolymerID... | method to build a molecule for a single polymer |
141,727 | private static RgroupStructure buildMoleculefromCHEM ( final String id , final List < Monomer > validMonomers ) throws BuilderMoleculeException , ChemistryException { LOG . info ( "Build molecule for chemical component" ) ; if ( validMonomers . size ( ) == 1 ) { try { Monomer monomer = validMonomers . get ( 0 ) ; Strin... | method to build a molecule from a chemical component |
141,728 | private static AttachmentList generateAttachmentList ( final List < Attachment > listAttachments ) { AttachmentList list = new AttachmentList ( ) ; for ( Attachment attachment : listAttachments ) { list . add ( new org . helm . chemtoolkit . Attachment ( attachment . getAlternateId ( ) , attachment . getLabel ( ) , att... | method to generate the AttachmentList given a list of attachments |
141,729 | public static AbstractMolecule mergeRgroups ( AbstractMolecule molecule ) throws BuilderMoleculeException , ChemistryException { try { boolean flag = true ; for ( int i = molecule . getAttachments ( ) . size ( ) - 1 ; i > - 1 ; i -- ) { org . helm . chemtoolkit . Attachment attachment = molecule . getAttachments ( ) . ... | method to merge all unused rgroups into a molecule |
141,730 | public static AbstractMolecule getMoleculeForMonomer ( final Monomer monomer ) throws BuilderMoleculeException , ChemistryException { String input = getInput ( monomer ) ; if ( input != null ) { List < Attachment > listAttachments = monomer . getAttachmentList ( ) ; AttachmentList list = new AttachmentList ( ) ; for ( ... | method to build a molecule for a given monomer |
141,731 | void addEntry ( final String aLine ) { final String trimmed = aLine . replaceAll ( "^>*" , "" ) ; String [ ] tokens = trimmed . split ( "\t" ) ; final Vector < String > v = new Vector < String > ( ) ; for ( int i = 0 ; i < tokens . length ; i ++ ) { if ( ! "" . equals ( tokens [ i ] ) ) { v . add ( tokens [ i ] ) ; } }... | as much of the file as possible . Currently about 70 entries are incorrect |
141,732 | public String getMatch ( final byte [ ] content ) throws IOException { final ByteBuffer buf = readBuffer ( content ) ; if ( buf == null ) { return null ; } buf . position ( 0 ) ; final boolean matches = match ( buf ) ; if ( matches ) { final int subLen = this . subEntries . size ( ) ; final String myMimeType = getMimeT... | Gets the match . |
141,733 | private int howManyGreaterThans ( final String aLine ) { if ( aLine == null ) { return - 1 ; } int i = 0 ; final int len = aLine . length ( ) ; while ( i < len ) { if ( aLine . charAt ( i ) == '>' ) { i ++ ; } else { break ; } } return i ; } | How many greater thans . |
141,734 | private boolean matchByte ( final ByteBuffer bbuf ) throws IOException { final byte b = bbuf . get ( 0 ) ; return b == getContent ( ) . charAt ( 0 ) ; } | Match byte . |
141,735 | private boolean matchLong ( final ByteBuffer bbuf , final ByteOrder bo , final boolean needMask , final long lMask ) throws IOException { bbuf . order ( bo ) ; long got ; final String testContent = getContent ( ) ; if ( testContent . startsWith ( "0x" ) ) { got = Long . parseLong ( testContent . substring ( 2 ) , 16 ) ... | Match long . |
141,736 | private boolean matchShort ( final ByteBuffer bbuf , final ByteOrder bo , final boolean needMask , final short sMask ) throws IOException { bbuf . order ( bo ) ; short got ; final String testContent = getContent ( ) ; if ( testContent . startsWith ( "0x" ) ) { got = ( short ) Integer . parseInt ( testContent . substrin... | Match short . |
141,737 | private boolean matchString ( final ByteBuffer bbuf ) throws IOException { if ( this . isBetween ) { final String buffer = new String ( bbuf . array ( ) ) ; if ( buffer . contains ( getContent ( ) ) ) { return true ; } return false ; } final int read = getContent ( ) . length ( ) ; for ( int j = 0 ; j < read ; j ++ ) {... | Match string . |
141,738 | @ SuppressWarnings ( "unused" ) private ByteBuffer readBuffer ( final RandomAccessFile raf ) throws IOException { final int startPos = getCheckBytesFrom ( ) ; if ( startPos > raf . length ( ) ) { return null ; } raf . seek ( startPos ) ; ByteBuffer buf ; switch ( getType ( ) ) { case MagicMimeEntry . STRING_TYPE : { in... | Read buffer . |
141,739 | public void traverseAndPrint ( final String tabs ) { logger . info ( tabs + toString ( ) ) ; final int len = this . subEntries . size ( ) ; for ( int i = 0 ; i < len ; i ++ ) { final MagicMimeEntry me = this . subEntries . get ( i ) ; me . traverseAndPrint ( tabs + "\t" ) ; } } | Traverse and print . |
141,740 | public void addEmptyValue ( final JKTableColumn col ) { final JKTableColumnValue value = new JKTableColumnValue ( col ) ; this . columnsValues . add ( value ) ; } | Adds the empty value . |
141,741 | public Double getColumnValueAsDouble ( final int col , final double defaultValue ) { Double value = getColumnValueAsDouble ( col ) ; if ( value == null ) { value = defaultValue ; } return value ; } | Gets the column value as double . |
141,742 | public static String getSMILESForAll ( HELM2Notation helm2notation ) throws BuilderMoleculeException , CTKException , ChemistryException { LOG . debug ( "Build single molecule(s)" ) ; List < AbstractMolecule > molecules = BuilderMolecule . buildMoleculefromPolymers ( helm2notation . getListOfPolymers ( ) , HELM2Notatio... | method to generate smiles for the whole HELMNotation |
141,743 | public static boolean containsGenericStructurePolymer ( List < PolymerNotation > polymers ) throws HELM2HandledException , ChemistryException , IOException , CTKException { for ( PolymerNotation polymer : polymers ) { if ( polymer . getPolymerID ( ) instanceof ChemEntity ) { Monomer monomer = MethodsMonomerUtils . getL... | method if the any of the given PolymerNotation contains generic structures |
141,744 | public static String getCanonicalSMILESForPolymer ( PolymerNotation polymer ) throws BuilderMoleculeException , HELM2HandledException , CTKSmilesException , CTKException , NotationException , ChemistryException { AbstractMolecule molecule = BuilderMolecule . buildMoleculefromSinglePolymer ( polymer ) . getMolecule ( ) ... | method to generate canonical smiles for one single PolymerNotation |
141,745 | public static String convertMolToSMILESWithAtomMapping ( String molfile , List < Attachment > attachments ) throws CTKException , ChemistryException { String smiles = Chemistry . getInstance ( ) . getManipulator ( ) . convertMolIntoSmilesWithAtomMapping ( molfile ) ; for ( Attachment attachment : attachments ) { int r ... | Converts molfile with the given attachments in smiles with atom mapping |
141,746 | public static boolean isConnected ( String molfile ) throws CTKException , ChemistryException { return Chemistry . getInstance ( ) . getManipulator ( ) . isConnected ( molfile ) ; } | returns if structure is connected |
141,747 | protected static CloseableHttpResponse putResource ( String json , String fullURL ) throws ClientProtocolException , IOException , URISyntaxException { try ( CloseableHttpClient httpclient = HttpClients . createDefault ( ) ) { HttpPut httpput = new HttpPut ( new URIBuilder ( fullURL ) . build ( ) ) ; httpput . setHeade... | Calls a PUT routine with given JSON on given resource URL . |
141,748 | protected static CloseableHttpResponse getResource ( String fullURL ) throws IOException , URISyntaxException { URI uri = new URIBuilder ( fullURL ) . build ( ) ; try ( CloseableHttpClient httpclient = HttpClients . createDefault ( ) ) { HttpGet httpget = new HttpGet ( uri ) ; LOG . debug ( "Executing request " + httpg... | Call a GET routine on given resource URL . |
141,749 | public static String getXHELM ( HELM2Notation helm2notation ) throws MonomerException , HELM1FormatException , IOException , JDOMException , NotationException , CTKException , ValidationException , ChemistryException { set = new HashSet < Monomer > ( ) ; Element root = new Element ( xHelmNotationExporter . XHELM_ELEMEN... | method to get xhelm for the helm notation only if it was possible to convert the helm in the old format |
141,750 | private static void addAdHocMonomer ( MonomerNotation monomerNotation ) throws IOException , JDOMException , ChemistryException { Monomer monomer = MonomerFactory . getInstance ( ) . getMonomerStore ( ) . getMonomer ( monomerNotation . getType ( ) , monomerNotation . getUnit ( ) . replace ( "[" , "" ) . replace ( "]" ,... | method to add the monomer to the database if it is an adhoc monomer |
141,751 | private List < Attachment > deserializeAttachmentList ( JsonParser parser , Map < String , Attachment > attachmentDB ) throws JsonParseException , IOException { List < Attachment > attachments = new ArrayList < Attachment > ( ) ; Attachment currentAttachment = null ; while ( ! JsonToken . END_ARRAY . equals ( parser . ... | Private routine to deserialize a JSON containing attachment data . This is done manually to give more freedom regarding data returned by the webservice . |
141,752 | private static List < CategorizedMonomer > deserializeEditorCategorizationConfig ( JsonParser parser ) throws JsonParseException , IOException { List < CategorizedMonomer > config = new LinkedList < CategorizedMonomer > ( ) ; CategorizedMonomer currentMonomer = null ; parser . nextToken ( ) ; while ( parser . hasCurren... | Private routine to deserialize JSON containing monomer categorization data . This is done manually to give more freedom regarding data returned by the webservice . |
141,753 | public static Attachment getAttachment ( Element attachment ) { Namespace ns = attachment . getNamespace ( ) ; Attachment att = new Attachment ( ) ; att . setAlternateId ( attachment . getChildText ( ATTACHEMENT_ID_ELEMENT , ns ) ) ; att . setLabel ( attachment . getChildText ( ATTACHEMENT_LABEL_ELEMENT , ns ) ) ; att ... | Convert ATTACHMENT element to Attachment object |
141,754 | public static Element getAttachementElement ( Attachment att ) { Element attachment = new Element ( ATTACHEMENT_ELEMENT ) ; if ( null != att . getAlternateId ( ) && att . getAlternateId ( ) . length ( ) > 0 ) { Element e = new Element ( ATTACHEMENT_ID_ELEMENT ) ; e . setText ( att . getAlternateId ( ) ) ; attachment . ... | This method converts Attachment to ATTACHMENT XML element |
141,755 | public static boolean validateAttachement ( Attachment attachment ) throws MonomerException , IOException , ChemistryException { String alternateId = attachment . getAlternateId ( ) ; if ( null == alternateId ) { throw new MonomerException ( "Attachment must have unique ID" ) ; } String smiles = attachment . getCapGrou... | This method validates Attachment by the following rules Attachment must have unique ID cap group SMILES must be valid cap group SMILES must contain one R group R group in SMILES must match R group label |
141,756 | public static Monomer getMonomer ( Element monomer ) throws MonomerException { Monomer m = new Monomer ( ) ; Namespace ns = monomer . getNamespace ( ) ; m . setAlternateId ( monomer . getChildText ( MONOMER_ID_ELEMENT , ns ) ) ; m . setCanSMILES ( monomer . getChildText ( MONOMER_SMILES_ELEMENT , ns ) ) ; String encode... | Convert monomer element to Monomer object |
141,757 | public static Element getMonomerElement ( Monomer monomer ) throws MonomerException { Element element = new Element ( MONOMER_ELEMENT ) ; if ( null != monomer . getAlternateId ( ) ) { Element e = new Element ( MONOMER_ID_ELEMENT ) ; e . setText ( monomer . getAlternateId ( ) ) ; element . getChildren ( ) . add ( e ) ; ... | This method converts Monomer to MONOMER XML element |
141,758 | private static boolean areAttachmentLabelsUnique ( List < String > labels ) { Map < String , String > map = new TreeMap < String , String > ( String . CASE_INSENSITIVE_ORDER ) ; for ( int i = 0 ; i < labels . size ( ) ; i ++ ) { map . put ( labels . get ( i ) , labels . get ( i ) ) ; } if ( labels . size ( ) == map . s... | This method checks if strings in a list are unique |
141,759 | public Attachment getAttachment ( String label ) { for ( Attachment attachment : attachmentList ) { if ( attachment . getLabel ( ) . equalsIgnoreCase ( label ) ) { return attachment ; } } return null ; } | get a specific attachment by passing in a label |
141,760 | public MoleculeProperty getCapMoleculeInfo ( String label ) throws CTKException , ChemistryException , IOException { for ( Attachment attachment : attachmentList ) { if ( attachment . getLabel ( ) . equalsIgnoreCase ( label ) ) { String capSmi = attachment . getCapGroupSMILES ( ) ; org . helm . chemtoolkit . MoleculeIn... | This method returns the MoleculeInfo for the input R group label of this monomer |
141,761 | public boolean addAttachment ( Attachment attachment ) { boolean isExist = false ; for ( Attachment a : attachmentList ) { if ( a . getLabel ( ) . equalsIgnoreCase ( attachment . getLabel ( ) ) ) { isExist = true ; } } if ( ! isExist ) { return attachmentList . add ( attachment ) ; } return false ; } | Try to add a new attachment to this monomer |
141,762 | public static JKCacheManager getCacheManager ( ) { if ( JKCacheFactory . defaultCacheManager == null ) { logger . debug ( "init cacheManager" ) ; defaultCacheManager = new JKDefaultCacheManager ( ) ; } return JKCacheFactory . defaultCacheManager ; } | Gets the default cache manager . |
141,763 | public JKTableColumn getTableColumn ( final int col , final boolean visibleIndex ) { int actualIndex ; if ( visibleIndex ) { actualIndex = this . visibilityManager . getActualIndexFromVisibleIndex ( col ) ; } else { actualIndex = col ; } return this . tableColumns . get ( actualIndex ) ; } | return NULL of col is out of bound . |
141,764 | public int getValueAtAsInteger ( final int row , final int col ) { final Object valueAt = getValueAt ( row , col ) ; int number = 0 ; if ( valueAt != null && ! valueAt . toString ( ) . equals ( "" ) ) { number = Integer . parseInt ( valueAt . toString ( ) . trim ( ) ) ; } return number ; } | Gets the value at as integer . |
141,765 | public boolean isEditable ( final int row , final int column ) { if ( isEditable ( column ) ) { final int actualIndex = getTableColumn ( column ) . getIndex ( ) ; final JKTableRecord record = getRecord ( row ) ; return record . isColumnEnabled ( actualIndex ) ; } return false ; } | Checks if is editable . |
141,766 | public void setEditable ( final int row , final int col , final boolean enable ) { final int actualIndex = getTableColumn ( col ) . getIndex ( ) ; getRecord ( row ) . setColumnEnabled ( actualIndex , enable ) ; } | Sets the editable . |
141,767 | public void addJKTableColumn ( String keyLabel ) { JKTableColumn col = new JKTableColumn ( ) ; col . setName ( keyLabel ) ; addJKTableColumn ( col ) ; } | Adds the JK table column . |
141,768 | public void insertConstructor ( InsertableConstructor insertableConstructor ) throws CannotCompileException , AfterBurnerImpossibleException , NotFoundException { List < CtConstructor > constructorList = extractExistingConstructors ( insertableConstructor ) ; log . info ( "constructor : " + constructorList . toString (... | Inserts java instructions into all constructors a given class . |
141,769 | protected ValidationResult getCachedResult ( String certFingerprint ) { CachedValidationResult cvr = validationResultsCache . get ( certFingerprint ) ; if ( cvr == null ) return null ; if ( ! cachedValidationResultHasExpired ( cvr , System . currentTimeMillis ( ) ) ) { return cvr . getResult ( ) ; } validationResultsCa... | Gets a validation result from the memory cache |
141,770 | public ValidationResult validate ( X509Certificate [ ] certChain ) { certChainSanityChecks ( certChain ) ; String certFingerprint = null ; try { certFingerprint = FingerprintHelper . getFingerprint ( certChain [ certChain . length - 1 ] ) ; } catch ( Throwable t ) { String errorMsg = String . format ( "Error computing ... | Validates a certificate chain using the wrapped validator caching the result for future validation calls . |
141,771 | public int minChannel ( ) { int c = 0 ; if ( getValue ( c ) > getValue ( 1 ) ) c = 1 ; if ( getValue ( c ) > getValue ( 2 ) ) c = 2 ; return c ; } | Returns the channel index with minimum value . Alpha is not considered . |
141,772 | public int maxChannel ( ) { int c = 0 ; if ( getValue ( c ) < getValue ( 1 ) ) c = 1 ; if ( getValue ( c ) < getValue ( 2 ) ) c = 2 ; return c ; } | Returns the channel index with maximum value . Alpha is not considered . |
141,773 | public JsTopicControls getJsTopicControlsFromProxyClass ( Class < ? > proxy ) { Class < ? > realClass = unProxyClassServices . getRealClass ( proxy ) ; return realClass . getAnnotation ( JsTopicControls . class ) ; } | get JsTopicControls from JsTopicAccessController instance |
141,774 | public void readStacktraceConfig ( @ Initialized ( ApplicationScoped . class ) ServletContext sc ) { String stacktrace ; if ( ocelotConfigurationsStack . isUnsatisfied ( ) ) { stacktrace = sc . getInitParameter ( Constants . Options . STACKTRACE_LENGTH ) ; if ( stacktrace == null ) { stacktrace = DEFAULTSTACKTRACE ; } ... | Read in web . xml the optional STACKTRACE_LENGTH config and set it in StacktraceConfigurationManager |
141,775 | public static String generateBasepath ( final String ip , Short port ) { if ( isEmpty ( ip ) ) { throw new IllegalArgumentException ( NULL_SERVER_IP_MSG ) ; } if ( port == null ) { port = 80 ; } StringBuilder basePath = new StringBuilder ( ) ; basePath . append ( "http://" ) . append ( ip ) . append ( ":" ) . append ( ... | Generate the base path for the retina . |
141,776 | public Object convertJsonToJava ( String jsonArg , Type paramType , Annotation [ ] parameterAnnotations ) throws JsonUnmarshallingException , JsonMarshallerException { if ( "null" . equals ( jsonArg ) ) { return null ; } JsonUnmarshaller juma = getJsonUnmarshallerAnnotation ( parameterAnnotations ) ; if ( null != juma ... | Convert json to Java |
141,777 | JsonUnmarshaller getJsonUnmarshallerAnnotation ( Annotation [ ] annotations ) { for ( Annotation annotation : annotations ) { if ( JsonUnmarshaller . class . isInstance ( annotation ) ) { return ( JsonUnmarshaller ) annotation ; } } return null ; } | return the JsonUnmarshaller annotation |
141,778 | Class < ? extends IJsonMarshaller > getMarshallerAnnotation ( Annotation [ ] annotations ) { JsonUnmarshaller ju = getJsonUnmarshallerAnnotation ( annotations ) ; return ( ju != null ) ? ju . value ( ) : null ; } | If argument is annotated with JsonUnmarshaller annotation get the JsonUnmarshaller class |
141,779 | Object convertArgument ( String arg , Type paramType ) throws IllegalArgumentException { Object result = null ; if ( null == arg || "null" . equals ( arg ) ) { return result ; } logger . debug ( "Try to convert {} : param = {} : {}" , new Object [ ] { arg , paramType , paramType . getClass ( ) } ) ; try { if ( Paramete... | try to convert json argument in java type |
141,780 | void checkStringArgument ( Class cls , String arg ) throws IOException { if ( arg . startsWith ( Constants . QUOTE ) ) { if ( ! cls . equals ( String . class ) ) { throw new IOException ( ) ; } } else if ( cls . equals ( String . class ) ) { throw new IOException ( ) ; } } | check if class and argument are string |
141,781 | private void compareApiUsage ( ) throws ApiException , JsonProcessingException { LOG . info ( "The Compare API usage." ) ; Compare compareApiInstance = retinaApisInstance . compareApi ( ) ; LOG . info ( "Compare API: compare" ) ; Metric metric = compareApiInstance . compare ( new Term ( "apple" ) , new Term ( "banana" ... | The Compare API usage . |
141,782 | private void imageApiUsage ( ) throws ApiException , IOException { LOG . info ( "The Image API usage." ) ; Images api = retinaApisInstance . imageApi ( ) ; LOG . info ( "Image API: getImageForExpression" ) ; try ( ByteArrayInputStream inputStream = api . getImage ( TEXT_1 ) ) { if ( inputStream . read ( ) == 0 ) { thro... | The Image API usage . |
141,783 | private void retinasApiUsage ( ) throws ApiException { LOG . info ( "The Retinas API usage." ) ; Retinas api = getInfo ( "api.cortical.io" , API_KEY ) ; LOG . info ( "Retinas API: getRetinas" ) ; List < Retina > retinas = api . getAllRetinas ( ) ; for ( Retina retina : retinas ) { LOG . info ( "Retina: Name: " + retin... | The Retinas API usage . |
141,784 | private void termsApiUsage ( ) throws JsonProcessingException , ApiException { LOG . info ( "The Terms API usage." ) ; Terms api = retinaApisInstance . termsApi ( ) ; LOG . info ( "Terms API: getContextsForTerm" ) ; List < Context > contexts = api . getContexts ( "apple" ) ; logContext ( contexts ) ; contexts = api . g... | The Terms API usage . |
141,785 | private void textApiUsage ( ) throws ApiException , JsonProcessingException { String text = "Toll IPEC has been an industry leader in environmental sustainability through its purchase of compressed natural gas powered trucks" ; String text2 = "Shellshock can serve as a highway for worms and malware to hit your Unix, Li... | The Text API usage . |
141,786 | public void doEvents ( ) { while ( ! isInterrupted ( ) ) { Iterator < Map . Entry < Timer , Runnable > > it = timerMap . entrySet ( ) . iterator ( ) ; if ( it . hasNext ( ) ) { long timeout = it . next ( ) . getKey ( ) . uptime - System . currentTimeMillis ( ) ; doEvents ( timeout > 0 ? timeout : 0 ) ; } else { doEvent... | Consume events until interrupted |
141,787 | public < T > T getField ( String field , ExtensionFieldType < T > extensionFieldType ) { if ( field == null || field . isEmpty ( ) ) { throw new IllegalArgumentException ( "Invalid field name" ) ; } if ( extensionFieldType == null ) { throw new IllegalArgumentException ( "Invalid field type" ) ; } if ( ! isFieldPresent... | Return the value for the field with a given name and type . |
141,788 | protected List getProjectClasspathElements ( ) throws DependencyResolutionRequiredException { Set results = new LinkedHashSet ( ) ; Set includes = getClasspathIncludes ( ) ; if ( includes . contains ( CLASSPATH_INCLUDE_ALL ) || includes . contains ( CLASSPATH_INCLUDE_RUNTIME ) ) { for ( Iterator i = project . getRuntim... | Allow the script to work with every JAR dependency of both the project and plugin including optional and provided dependencies . Runtime classpath elements are loaded first so that legacy behavior is not modified . Additional elements are added first in the order of project artifacts then in the order of plugin artifac... |
141,789 | private Map findProviders ( ) { Map providers = getContainer ( ) . getComponentDescriptorMap ( Provider . class . getName ( ) ) ; if ( providers == null ) { throw new Error ( "No providers discovered" ) ; } Set keys = providers . keySet ( ) ; Map found = null ; for ( Iterator iter = keys . iterator ( ) ; iter . hasNext... | Find any providers which are available in the container . |
141,790 | void writeDependencies ( Writer writer , String deco , String ... dependencies ) throws IOException { boolean first = true ; for ( String dependency : dependencies ) { if ( ! first ) { writer . append ( COMMA ) . append ( SPACEOPTIONAL ) ; } writer . append ( deco ) . append ( dependency ) . append ( deco ) ; first = f... | dep1 dep2 or if deco = dep1 dep2 |
141,791 | public void writeCloseFunction ( Writer writer ) throws IOException { writer . append ( TAB ) . append ( CLOSEBRACE ) . append ( CR ) ; } | \ t } |
141,792 | void writeArguments ( Iterator < String > names , Writer writer ) throws IOException { while ( names . hasNext ( ) ) { String name = names . next ( ) ; writer . append ( name ) ; if ( names . hasNext ( ) ) { writer . append ( COMMA ) . append ( SPACEOPTIONAL ) ; } } } | Write argument whit comma if necessary |
141,793 | void writeReturnComment ( TypeMirror returnType , Writer writer ) throws IOException { String type = returnType . toString ( ) ; if ( ! "void" . equals ( type ) ) { writer . append ( TAB2 ) . append ( " * @return " ) . append ( OPENBRACE ) . append ( type ) . append ( CLOSEBRACE ) . append ( CR ) ; } } | write js documentation for return type |
141,794 | void writeArgumentsComment ( Iterator < String > argumentsType , Iterator < String > argumentsName , Writer writer ) throws IOException { while ( argumentsType . hasNext ( ) ) { String type = argumentsType . next ( ) ; String name = argumentsName . next ( ) ; writer . append ( TAB2 ) . append ( " * @param " ) . append ... | write js documentation for arguments |
141,795 | void writeJavadocComment ( String methodComment , Writer writer ) throws IOException { if ( methodComment != null ) { methodComment = methodComment . split ( "@" ) [ 0 ] ; int lastIndexOf = methodComment . lastIndexOf ( "\n" ) ; if ( lastIndexOf >= 0 ) { methodComment = methodComment . substring ( 0 , lastIndexOf ) ; }... | write js documentation from javadoc |
141,796 | void createMethodBody ( String classname , ExecutableElement methodElement , List < String > arguments , Writer writer ) throws IOException { String methodName = getMethodName ( methodElement ) ; boolean ws = isWebsocketDataService ( methodElement ) ; String args = stringJoinAndDecorate ( arguments , COMMA , new Nothin... | Create javascript method body |
141,797 | String computeKeys ( ExecutableElement methodElement , List < String > arguments ) { String keys = stringJoinAndDecorate ( arguments , COMMA , new NothingDecorator ( ) ) ; if ( arguments != null && ! arguments . isEmpty ( ) ) { JsCacheResult jcr = methodElement . getAnnotation ( JsCacheResult . class ) ; if ( ! conside... | Generate key part for variable part of md5 |
141,798 | void createReturnOcelotPromiseFactory ( String classname , String methodName , boolean ws , String args , String keys , Writer writer ) throws IOException { String md5 = keyMaker . getMd5 ( classname + DOT + methodName ) ; writer . append ( TAB3 ) . append ( "return promiseFactory.create" ) . append ( OPENPARENTHESIS )... | Return body js line that return the OcelotPromise |
141,799 | String stringJoinAndDecorate ( final List < String > list , final String sep , StringDecorator decorator ) { if ( decorator == null ) { decorator = new NothingDecorator ( ) ; } StringBuilder sb = new StringBuilder ( ) ; if ( list != null ) { boolean first = true ; for ( String argument : list ) { if ( ! first ) { sb . ... | Join list and separate by sep each elements is decorate by decorator |
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