idx int64 0 41.2k | question stringlengths 83 4.15k | target stringlengths 5 715 |
|---|---|---|
18,000 | public static void scan ( final Class < ? extends Annotation > clas , final String [ ] basePackage , final AnnotationHandler handler ) { final ClassPathScanningCandidateComponentProvider scanner = new ClassPathScanningCandidateComponentProvider ( false ) ; scanner . setResourceLoader ( new PathMatchingResourcePatternResolver ( Thread . currentThread ( ) . getContextClassLoader ( ) ) ) ; scanner . addIncludeFilter ( new AnnotationTypeFilter ( clas ) ) ; for ( final String pck : basePackage ) { for ( final BeanDefinition bd : scanner . findCandidateComponents ( pck ) ) { handler . handleAnnotationFound ( bd . getBeanClassName ( ) ) ; } } } | Utility method to scan the given package and handler for the annotation of the given class . Its uses the Spring annotation detector |
18,001 | public static List < String > scanAsList ( final Class < ? extends Annotation > clas , final String ... basePackage ) { final List < String > classes = new ArrayList < > ( ) ; scan ( clas , basePackage , new AnnotationHandler ( ) { public void handleAnnotationFound ( String className ) { classes . add ( className ) ; } } ) ; return classes ; } | Scan as list . |
18,002 | public void refreshGuiAndShowFile ( File file ) { if ( rootNode . getChildCount ( ) > 0 ) { rootNode . removeAllChildren ( ) ; treeModel . reload ( ) ; } if ( guiMain . getAsmProjectUml ( ) . getProjectUml ( ) != null ) { addTreeNodes ( file ) ; guiMain . getMenuMain ( ) . setVisibleProjectMenu ( true ) ; } else { guiMain . getMenuMain ( ) . setVisibleProjectMenu ( false ) ; } } | refresh tree and expand to file that usually newly created |
18,003 | public static String buildToString ( Object ... params ) { StringBuffer finalMessage = new StringBuffer ( ) ; int i = 0 ; for ( Object object : params ) { if ( i ++ > 0 ) { finalMessage . append ( FIELD_SEPARATOR ) ; } if ( object instanceof List < ? > ) { finalMessage . append ( JKCollectionUtil . toString ( ( List < ? > ) object ) ) ; } else { finalMessage . append ( JKObjectUtil . toString ( object , true ) ) ; } } String fullText = finalMessage . toString ( ) ; return fullText ; } | Builds the to string . |
18,004 | public static Map toMap ( Object [ ] keys , Object [ ] values ) { Map map = new HashMap < > ( ) ; int i = 0 ; for ( Object key : keys ) { map . put ( key , values [ i ++ ] ) ; } return map ; } | To map . |
18,005 | public static void validateNull ( String name , Object object ) { if ( object == null ) { throw new IllegalStateException ( name . concat ( " cannot be null" ) ) ; } } | Validate null . |
18,006 | public static void addToSystemConfig ( String prefix , Properties prop ) { for ( Entry < Object , Object > entry : prop . entrySet ( ) ) { String key = prefix . concat ( entry . getKey ( ) . toString ( ) ) ; String value = entry . getValue ( ) . toString ( ) ; System . setProperty ( key , value ) ; } } | Adds the to system config . |
18,007 | public static char [ ] readPassword ( String msg ) { Console console = System . console ( ) ; if ( console != null ) { return console . readPassword ( ) ; } scanner = getScanner ( ) ; System . out . print ( msg ) ; return scanner . nextLine ( ) . toCharArray ( ) ; } | Read password . |
18,008 | public static void printOnce ( Object msg ) { if ( messagesCache . get ( msg . hashCode ( ) ) == null ) { JK . printBlock ( msg ) ; messagesCache . put ( msg . hashCode ( ) , msg ) ; } } | Print the message and then save it into list to avoid reporing it again it can be helpfull to debugging purposes . |
18,009 | public static String getAppName ( ) { String appName = System . getProperty ( JKContextConstants . JK_APP_NAME ) ; if ( appName == null ) { String mainClassName = JKDebugUtil . getMainClassName ( ) ; return mainClassName . substring ( 0 , mainClassName . lastIndexOf ( "." ) ) ; } return appName ; } | Gets the app name . |
18,010 | 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 ( ) . getName ( ) ) ; } } | Dump beans names . |
18,011 | 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 ) ; } return cfg ; } | Gets the config . |
18,012 | 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 . |
18,013 | 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 . |
18,014 | private void resetConfigToDefault ( ) { isUseWebservice = true ; isUpdateAutomatic = true ; isUseExternalMonomers = false ; isUseExternalNucleotides = false ; setUseExternalAttachments ( false ) ; webserviceMonomersURL = "http://localhost:8080/HELM2MonomerService/rest" ; webserviceMonomersPath = "monomer/" ; webserviceMonomersPutPath = "monomer/" ; webserviceEditorCategorizationURL = "http://localhost:8080" ; webserviceEditorCategorizationPath = "" ; externalNucleotidesPath = "" ; externalMonomersPath = "" ; setExternalAttachmentsPath ( "" ) ; } | Resets the configuration to default values . |
18,015 | 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.properties" ) ; reader = new BufferedReader ( new InputStreamReader ( in ) ) ; writer = new BufferedWriter ( new FileWriter ( configFile ) ) ; String line ; while ( ( line = reader . readLine ( ) ) != null ) { writer . write ( line + System . getProperty ( "line.separator" ) ) ; } } catch ( Exception e ) { resetConfigToDefault ( ) ; e . printStackTrace ( ) ; } finally { try { if ( writer != null ) { writer . close ( ) ; } if ( reader != null ) { reader . close ( ) ; } } catch ( IOException e ) { e . printStackTrace ( ) ; } } } try { PropertiesConfiguration conf = new PropertiesConfiguration ( CONFIG_FILE_PATH ) ; isUseWebservice = conf . getBoolean ( USE_WEBSERVICE ) ; isUpdateAutomatic = conf . getBoolean ( UPDATE_AUTOMATIC ) ; webserviceMonomersURL = conf . getString ( WEBSERVICE_MONOMERS_URL ) ; webserviceMonomersPath = conf . getString ( WEBSERVICE_MONOMERS_PATH ) ; webserviceMonomersPutPath = conf . getString ( WEBSERVICE_MONOMERS_PUT_PATH ) ; webserviceNucleotidesURL = conf . getString ( WEBSERVICE_NUCLEOTIDES_URL ) ; webserviceNucleotidesPath = conf . getString ( WEBSERVICE_NUCLEOTIDES_PATH ) ; webserviceNucleotidesPutPath = conf . getString ( WEBSERVICE_NUCLEOTIDES_PUT_PATH ) ; webserviceEditorCategorizationURL = conf . getString ( WEBSERVICE_EDITOR_CATEGORIZATION_URL ) ; webserviceEditorCategorizationPath = conf . getString ( WEBSERVICE_EDITOR_CATEGORIZATION_PATH ) ; isUseExternalMonomers = conf . getBoolean ( USE_EXTERNAL_MONOMERS ) ; externalMonomersPath = conf . getString ( EXTERNAL_MONOMERS_PATH ) ; isUseExternalNucleotides = conf . getBoolean ( USE_EXTERNAL_NUCLEOTIDES ) ; externalNucleotidesPath = conf . getString ( EXTERNAL_NUCLEOTIDES_PATH ) ; isUseExternalAttachments = conf . getBoolean ( USE_EXTERNAL_ATTACHMENTS ) ; externalAttachmentsPath = conf . getString ( EXTERNAL_ATTACHMENTS_PATH ) ; } catch ( ConfigurationException | NoSuchElementException e ) { resetConfigToDefault ( ) ; e . printStackTrace ( ) ; } } | Refreshes the configuration using the local properties file . |
18,016 | 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 . |
18,017 | 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 ; } } return null ; } | Gets the magic mime type . |
18,018 | 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 . |
18,019 | 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 . length ( ) == 0 || line . charAt ( 0 ) == '#' ) { line = br . readLine ( ) ; continue ; } sequence . add ( line ) ; while ( true ) { line = br . readLine ( ) ; if ( line == null ) { addEntry ( sequence ) ; sequence . clear ( ) ; break ; } line = line . trim ( ) ; if ( line . length ( ) == 0 || line . charAt ( 0 ) == '#' ) { continue ; } if ( line . charAt ( 0 ) != '>' ) { addEntry ( sequence ) ; sequence . clear ( ) ; break ; } sequence . add ( line ) ; } } if ( ! sequence . isEmpty ( ) ) { addEntry ( sequence ) ; } } | Parse the magic . mime file |
18,020 | 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 . |
18,021 | 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 whole HELMNotation the smiles representation" ) ; AbstractMolecule molecule = Chemistry . getInstance ( ) . getManipulator ( ) . getMolecule ( smiles , null ) ; LOG . info ( "Molecule was created using the smiles generation" ) ; String molFile = Chemistry . getInstance ( ) . getManipulator ( ) . convertMolecule ( molecule , AbstractChemistryManipulator . StType . MOLFILE ) ; LOG . info ( "Generate molfile for the built molecule(s)" ) ; return Chemistry . getInstance ( ) . getManipulator ( ) . renderMol ( molFile , OutputType . PNG , PICTURE_WIDTH , PICTURE_HEIGHT , ( int ) Long . parseLong ( "D3D3D3" , 16 ) ) ; } | method to generate an image of the HELM molecule |
18,022 | 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 ) ; Map < String , Monomer > peptideMap = MonomerFactory . getInstance ( ) . getMonomerDB ( ) . get ( Monomer . PEPTIDE_POLYMER_TYPE ) ; Set < String > keySet = peptideMap . keySet ( ) ; List < String > l = new ArrayList < String > ( ) ; int pos = 0 ; while ( pos < cleanSeq . length ( ) ) { boolean found = false ; for ( Iterator i = keySet . iterator ( ) ; i . hasNext ( ) ; ) { String symbol = ( String ) i . next ( ) ; if ( cleanSeq . startsWith ( symbol , pos ) ) { found = true ; l . add ( symbol ) ; pos = pos + symbol . length ( ) ; break ; } } if ( ! found ) { throw new NotationException ( "Sequence contains unknown amino acid starting at " + cleanSeq . substring ( pos ) ) ; } } return l ; } | This method converts peptide sequence into a List of amino acid |
18,023 | 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 || delimiter . length ( ) == 0 ) { return getAminoAcidList ( peptideSequence ) ; } else { if ( ! isValidDelimiter ( delimiter ) ) throw new NotationException ( "Invalid sequence delimiter [" + delimiter + "], only the following are supported: [" + getValidDelimiters ( ) + "]" ) ; } List < String > blocks = new ArrayList < String > ( ) ; StringTokenizer st = new StringTokenizer ( peptideSequence , delimiter ) ; while ( st . hasMoreTokens ( ) ) { blocks . add ( st . nextToken ( ) ) ; } List < String > l = new ArrayList < String > ( ) ; for ( String block : blocks ) { List < String > tmpL = getAminoAcidList ( block ) ; l . addAll ( tmpL ) ; } return l ; } | This method converts peptide sequence into a List of amino acid with optional delimiter |
18,024 | 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 |
18,025 | 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 . writeBytesToFile ( data , localFile ) ; } | Download file . |
18,026 | 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 . |
18,027 | 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 < ? > keys = header . keys ( ) ; while ( keys . hasMoreElements ( ) ) { final String key = ( String ) keys . nextElement ( ) ; connection . addRequestProperty ( key , header . getProperty ( key ) ) ; } connection . setDoOutput ( true ) ; final OutputStream out = connection . getOutputStream ( ) ; out . write ( body . getBytes ( ) ) ; connection . connect ( ) ; final int errorCode = connection . getResponseCode ( ) ; if ( errorCode != HttpURLConnection . HTTP_OK ) { throw new JKHttpException ( connection . getResponseMessage ( ) , errorCode ) ; } final String response = JKIOUtil . convertToString ( connection . getInputStream ( ) ) ; return response ; } catch ( IOException e ) { throw new JKHttpException ( e ) ; } } | Send http request . |
18,028 | 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 InputStreamReader ( inputStream ) ) ; StringBuffer contents = new StringBuffer ( ) ; String line ; while ( ( line = reader . readLine ( ) ) != null ) { contents . append ( line ) ; contents . append ( JK . NEW_LINE ) ; } inputStream . close ( ) ; return contents . toString ( ) ; } catch ( Exception e ) { JKExceptionUtil . handle ( e ) ; return null ; } finally { if ( con != null ) { con . disconnect ( ) ; } } } | Gets the url contents . |
18,029 | 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 substring ; } return null ; } | Gets the value from url based on pre - text value from the response . |
18,030 | 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 . |
18,031 | 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 . |
18,032 | 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 . |
18,033 | 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 . |
18,034 | public String getName ( ) { if ( name == null ) { name = JKMessage . get ( getJavaType ( ) . getSimpleName ( ) ) ; } return name ; } | Gets the name . |
18,035 | 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 ( timeInstance . get ( Calendar . MINUTE ) ) ; Calendar dateInstance = Calendar . getInstance ( ) ; dateInstance . setTime ( date ) ; fsTimeObject . setYear ( dateInstance . get ( Calendar . YEAR ) ) ; fsTimeObject . setMonth ( dateInstance . get ( Calendar . MONTH ) ) ; fsTimeObject . setDay ( dateInstance . get ( Calendar . DAY_OF_MONTH ) ) ; return fsTimeObject ; } | To time object . |
18,036 | public static RgroupStructure buildMoleculefromSinglePolymer ( final PolymerNotation polymernotation ) throws BuilderMoleculeException , HELM2HandledException , ChemistryException { LOG . info ( "Build molecule for single Polymer " + polymernotation . getPolymerID ( ) . getId ( ) ) ; if ( polymernotation . getPolymerID ( ) instanceof BlobEntity ) { LOG . error ( "Molecule can't be build for BLOB" ) ; throw new BuilderMoleculeException ( "Molecule can't be build for BLOB" ) ; } else if ( polymernotation . getPolymerID ( ) instanceof ChemEntity ) { List < Monomer > validMonomers = MethodsMonomerUtils . getListOfHandledMonomers ( polymernotation . getPolymerElements ( ) . getListOfElements ( ) ) ; return buildMoleculefromCHEM ( polymernotation . getPolymerID ( ) . getId ( ) , validMonomers ) ; } else if ( polymernotation . getPolymerID ( ) instanceof RNAEntity || polymernotation . getPolymerID ( ) instanceof PeptideEntity ) { List < Monomer > validMonomers = MethodsMonomerUtils . getListOfHandledMonomers ( polymernotation . getPolymerElements ( ) . getListOfElements ( ) ) ; return buildMoleculefromPeptideOrRNA ( polymernotation . getPolymerID ( ) . getId ( ) , validMonomers ) ; } else { LOG . error ( "Molecule can't be build for unknown polymer type" ) ; throw new BuilderMoleculeException ( "Molecule can't be build for unknown polymer type" ) ; } } | method to build a molecule for a single polymer |
18,037 | 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 ) ; String input = getInput ( monomer ) ; if ( input != null ) { List < Attachment > listAttachments = monomer . getAttachmentList ( ) ; AttachmentList list = new AttachmentList ( ) ; for ( Attachment attachment : listAttachments ) { list . add ( new org . helm . chemtoolkit . Attachment ( attachment . getAlternateId ( ) , attachment . getLabel ( ) , attachment . getCapGroupName ( ) , attachment . getCapGroupSMILES ( ) ) ) ; } AbstractMolecule molecule = Chemistry . getInstance ( ) . getManipulator ( ) . getMolecule ( input , list ) ; RgroupStructure result = new RgroupStructure ( ) ; result . setMolecule ( molecule ) ; result . setRgroupMap ( generateRgroupMap ( id + ":" + "1" , molecule ) ) ; return result ; } else { LOG . error ( "Chemical molecule should have canonical smiles" ) ; throw new BuilderMoleculeException ( "Chemical molecule should have canoncial smiles" ) ; } } catch ( NullPointerException ex ) { throw new BuilderMoleculeException ( "Monomer is not stored in the monomer database" ) ; } catch ( IOException | CTKException e ) { LOG . error ( "Molecule can't be built " + e . getMessage ( ) ) ; throw new BuilderMoleculeException ( "Molecule can't be built " + e . getMessage ( ) ) ; } } else { LOG . error ( "Chemical molecule should contain exactly one monomer" ) ; throw new BuilderMoleculeException ( "Chemical molecule should contain exactly one monomer" ) ; } } | method to build a molecule from a chemical component |
18,038 | 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 ( ) , attachment . getCapGroupName ( ) , attachment . getCapGroupSMILES ( ) ) ) ; } return list ; } | method to generate the AttachmentList given a list of attachments |
18,039 | 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 ( ) . get ( i ) ; int groupId = AbstractMolecule . getIdFromLabel ( attachment . getLabel ( ) ) ; AbstractMolecule rMol = Chemistry . getInstance ( ) . getManipulator ( ) . getMolecule ( attachment . getSmiles ( ) , null ) ; molecule = Chemistry . getInstance ( ) . getManipulator ( ) . merge ( molecule , molecule . getRGroupAtom ( groupId , true ) , rMol , rMol . getRGroupAtom ( groupId , true ) ) ; } return molecule ; } catch ( NullPointerException | IOException | CTKException e ) { throw new BuilderMoleculeException ( "Unused rgroups can't be merged into the molecule" + e . getMessage ( ) ) ; } } | method to merge all unused rgroups into a molecule |
18,040 | 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 ( Attachment attachment : listAttachments ) { list . add ( new org . helm . chemtoolkit . Attachment ( attachment . getAlternateId ( ) , attachment . getLabel ( ) , attachment . getCapGroupName ( ) , attachment . getCapGroupSMILES ( ) ) ) ; } try { return Chemistry . getInstance ( ) . getManipulator ( ) . getMolecule ( input , list ) ; } catch ( IOException | CTKException e ) { throw new BuilderMoleculeException ( "Molecule can't be built for the given monomer" ) ; } } return null ; } | method to build a molecule for a given monomer |
18,041 | 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 ] ) ; } } tokens = new String [ v . size ( ) ] ; tokens = v . toArray ( tokens ) ; if ( tokens . length > 0 ) { final String tok = tokens [ 0 ] . trim ( ) ; try { if ( tok . startsWith ( "0x" ) ) { this . checkBytesFrom = Integer . parseInt ( tok . substring ( 2 ) , 16 ) ; } else { this . checkBytesFrom = Integer . parseInt ( tok ) ; } } catch ( final NumberFormatException e ) { addEntry ( trimmed . replaceAll ( " " , "\t" ) ) ; return ; } } if ( tokens . length > 1 ) { this . typeStr = tokens [ 1 ] . trim ( ) ; this . type = getType ( this . typeStr ) ; } if ( tokens . length > 2 ) { this . content = ltrim ( tokens [ 2 ] ) ; this . content = stringWithEscapeSubstitutions ( this . content ) ; } if ( tokens . length > 3 ) { this . mimeType = tokens [ 3 ] . trim ( ) ; } if ( tokens . length > 4 ) { this . mimeEnc = tokens [ 4 ] . trim ( ) ; } } | as much of the file as possible . Currently about 70 entries are incorrect |
18,042 | 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 = getMimeType ( ) ; if ( subLen > 0 ) { String mtype = null ; for ( int k = 0 ; k < subLen ; k ++ ) { final MagicMimeEntry me = this . subEntries . get ( k ) ; mtype = me . getMatch ( content ) ; if ( mtype != null ) { return mtype ; } } if ( myMimeType != null ) { return myMimeType ; } } else { return myMimeType ; } } return null ; } | Gets the match . |
18,043 | 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 . |
18,044 | private boolean matchByte ( final ByteBuffer bbuf ) throws IOException { final byte b = bbuf . get ( 0 ) ; return b == getContent ( ) . charAt ( 0 ) ; } | Match byte . |
18,045 | 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 ) ; } else if ( testContent . startsWith ( "&" ) ) { got = Long . parseLong ( testContent . substring ( 3 ) , 16 ) ; } else { got = Long . parseLong ( testContent ) ; } long found = bbuf . getInt ( ) ; if ( needMask ) { found = ( short ) ( found & lMask ) ; } if ( got != found ) { return false ; } return true ; } | Match long . |
18,046 | 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 . substring ( 2 ) , 16 ) ; } else if ( testContent . startsWith ( "&" ) ) { got = ( short ) Integer . parseInt ( testContent . substring ( 3 ) , 16 ) ; } else { got = ( short ) Integer . parseInt ( testContent ) ; } short found = bbuf . getShort ( ) ; if ( needMask ) { found = ( short ) ( found & sMask ) ; } if ( got != found ) { return false ; } return true ; } | Match short . |
18,047 | 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 ++ ) { if ( ( bbuf . get ( j ) & 0xFF ) != getContent ( ) . charAt ( j ) ) { return false ; } } return true ; } | Match string . |
18,048 | @ 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 : { int len = 0 ; final int index = this . typeStr . indexOf ( ">" ) ; if ( index != - 1 ) { len = Integer . parseInt ( this . typeStr . substring ( index + 1 , this . typeStr . length ( ) - 1 ) ) ; this . isBetween = true ; } else { len = getContent ( ) . length ( ) ; } buf = ByteBuffer . allocate ( len + 1 ) ; raf . read ( buf . array ( ) , 0 , len ) ; break ; } case MagicMimeEntry . SHORT_TYPE : case MagicMimeEntry . LESHORT_TYPE : case MagicMimeEntry . BESHORT_TYPE : { buf = ByteBuffer . allocate ( 2 ) ; raf . read ( buf . array ( ) , 0 , 2 ) ; break ; } case MagicMimeEntry . LELONG_TYPE : case MagicMimeEntry . BELONG_TYPE : { buf = ByteBuffer . allocate ( 4 ) ; raf . read ( buf . array ( ) , 0 , 4 ) ; break ; } case MagicMimeEntry . BYTE_TYPE : { buf = ByteBuffer . allocate ( 1 ) ; raf . read ( buf . array ( ) , 0 , 1 ) ; } default : { buf = null ; break ; } } return buf ; } | Read buffer . |
18,049 | 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 . |
18,050 | public void addEmptyValue ( final JKTableColumn col ) { final JKTableColumnValue value = new JKTableColumnValue ( col ) ; this . columnsValues . add ( value ) ; } | Adds the empty value . |
18,051 | 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 . |
18,052 | public static String getSMILESForAll ( HELM2Notation helm2notation ) throws BuilderMoleculeException , CTKException , ChemistryException { LOG . debug ( "Build single molecule(s)" ) ; List < AbstractMolecule > molecules = BuilderMolecule . buildMoleculefromPolymers ( helm2notation . getListOfPolymers ( ) , HELM2NotationUtils . getAllEdgeConnections ( helm2notation . getListOfConnections ( ) ) ) ; LOG . debug ( "Built single molecule(s)" ) ; StringBuffer sb = new StringBuffer ( ) ; for ( AbstractMolecule molecule : molecules ) { molecule = BuilderMolecule . mergeRgroups ( molecule ) ; sb . append ( Chemistry . getInstance ( ) . getManipulator ( ) . convertMolecule ( molecule , AbstractChemistryManipulator . StType . SMILES ) + "." ) ; } sb . setLength ( sb . length ( ) - 1 ) ; LOG . debug ( "SMILES-All :" + sb . toString ( ) ) ; return sb . toString ( ) ; } | method to generate smiles for the whole HELMNotation |
18,053 | public static boolean containsGenericStructurePolymer ( List < PolymerNotation > polymers ) throws HELM2HandledException , ChemistryException , IOException , CTKException { for ( PolymerNotation polymer : polymers ) { if ( polymer . getPolymerID ( ) instanceof ChemEntity ) { Monomer monomer = MethodsMonomerUtils . getListOfHandledMonomers ( polymer . getPolymerElements ( ) . getListOfElements ( ) ) . get ( 0 ) ; if ( null == monomer . getCanSMILES ( ) || monomer . getCanSMILES ( ) . length ( ) == 0 ) { return true ; } if ( monomer . containAnyAtom ( ) ) { return true ; } } } return false ; } | method if the any of the given PolymerNotation contains generic structures |
18,054 | public static String getCanonicalSMILESForPolymer ( PolymerNotation polymer ) throws BuilderMoleculeException , HELM2HandledException , CTKSmilesException , CTKException , NotationException , ChemistryException { AbstractMolecule molecule = BuilderMolecule . buildMoleculefromSinglePolymer ( polymer ) . getMolecule ( ) ; molecule = BuilderMolecule . mergeRgroups ( molecule ) ; return Chemistry . getInstance ( ) . getManipulator ( ) . canonicalize ( Chemistry . getInstance ( ) . getManipulator ( ) . convertMolecule ( molecule , AbstractChemistryManipulator . StType . SMILES ) ) ; } | method to generate canonical smiles for one single PolymerNotation |
18,055 | 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 = Integer . valueOf ( attachment . getLabel ( ) . replaceAll ( "\\D+" , "" ) ) ; smiles = smiles . replace ( "[*:" + r + "]" , "[" + attachment . getCapGroupName ( ) + ":" + r + "]" ) ; } return smiles ; } | Converts molfile with the given attachments in smiles with atom mapping |
18,056 | public static boolean isConnected ( String molfile ) throws CTKException , ChemistryException { return Chemistry . getInstance ( ) . getManipulator ( ) . isConnected ( molfile ) ; } | returns if structure is connected |
18,057 | 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 . setHeader ( "Content-Type" , "application/json;charset=UTF-8" ) ; httpput . setEntity ( new StringEntity ( json , "UTF-8" ) ) ; LOG . debug ( "Executing request " + httpput . getRequestLine ( ) ) ; return httpclient . execute ( httpput ) ; } } | Calls a PUT routine with given JSON on given resource URL . |
18,058 | 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 " + httpget . getRequestLine ( ) ) ; return httpclient . execute ( httpget ) ; } } | Call a GET routine on given resource URL . |
18,059 | 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_ELEMENT ) ; Document doc = new Document ( root ) ; Element helmElement = new Element ( xHelmNotationExporter . HELM_NOTATION_ELEMENT ) ; helmElement . setText ( HELM1Utils . getStandard ( helm2notation ) ) ; root . addContent ( helmElement ) ; Element monomerListElement = new Element ( xHelmNotationExporter . MONOMER_LIST_ELEMENT ) ; for ( MonomerNotation monomernotation : MethodsMonomerUtils . getListOfMonomerNotation ( helm2notation . getListOfPolymers ( ) ) ) { if ( monomernotation instanceof MonomerNotationUnitRNA ) { for ( MonomerNotationUnit unit : ( ( MonomerNotationUnitRNA ) monomernotation ) . getContents ( ) ) { addAdHocMonomer ( unit ) ; } } else { addAdHocMonomer ( monomernotation ) ; } } for ( Monomer distinctmonomer : set ) { Element monomerElement = MonomerParser . getMonomerElement ( distinctmonomer ) ; monomerListElement . getChildren ( ) . add ( monomerElement ) ; } root . addContent ( monomerListElement ) ; XMLOutputter xmlOutput = new XMLOutputter ( ) ; xmlOutput . setFormat ( Format . getPrettyFormat ( ) ) ; return xmlOutput . outputString ( doc ) ; } | method to get xhelm for the helm notation only if it was possible to convert the helm in the old format |
18,060 | private static void addAdHocMonomer ( MonomerNotation monomerNotation ) throws IOException , JDOMException , ChemistryException { Monomer monomer = MonomerFactory . getInstance ( ) . getMonomerStore ( ) . getMonomer ( monomerNotation . getType ( ) , monomerNotation . getUnit ( ) . replace ( "[" , "" ) . replace ( "]" , "" ) ) ; if ( monomer . isAdHocMonomer ( ) ) { set . add ( monomer ) ; } } | method to add the monomer to the database if it is an adhoc monomer |
18,061 | 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 . nextToken ( ) ) ) { String fieldName = parser . getCurrentName ( ) ; JsonToken token = parser . getCurrentToken ( ) ; if ( JsonToken . START_OBJECT . equals ( token ) ) { currentAttachment = new Attachment ( ) ; } else if ( JsonToken . END_OBJECT . equals ( token ) ) { if ( AttachmentLoader . validateAttachment ( currentAttachment ) ) { currentAttachment . setCapGroupSMILES ( attachmentDB . get ( currentAttachment . getAlternateId ( ) ) . getCapGroupSMILES ( ) ) ; attachments . add ( currentAttachment ) ; } } if ( fieldName != null ) { switch ( fieldName ) { case "id" : parser . nextToken ( ) ; if ( parser . getText ( ) != null ) { currentAttachment . setId ( Integer . parseInt ( parser . getText ( ) ) ) ; } break ; case "alternateId" : parser . nextToken ( ) ; currentAttachment . setAlternateId ( parser . getText ( ) ) ; break ; case "label" : parser . nextToken ( ) ; currentAttachment . setLabel ( parser . getText ( ) ) ; break ; case "capGroupName" : parser . nextToken ( ) ; currentAttachment . setCapGroupName ( parser . getText ( ) ) ; break ; case "capGroupSMILES" : parser . nextToken ( ) ; currentAttachment . setCapGroupSMILES ( parser . getText ( ) ) ; break ; default : break ; } } } return attachments ; } | Private routine to deserialize a JSON containing attachment data . This is done manually to give more freedom regarding data returned by the webservice . |
18,062 | private static List < CategorizedMonomer > deserializeEditorCategorizationConfig ( JsonParser parser ) throws JsonParseException , IOException { List < CategorizedMonomer > config = new LinkedList < CategorizedMonomer > ( ) ; CategorizedMonomer currentMonomer = null ; parser . nextToken ( ) ; while ( parser . hasCurrentToken ( ) ) { String fieldName = parser . getCurrentName ( ) ; JsonToken token = parser . getCurrentToken ( ) ; if ( JsonToken . START_OBJECT . equals ( token ) ) { currentMonomer = new CategorizedMonomer ( ) ; } else if ( JsonToken . END_OBJECT . equals ( token ) ) { config . add ( currentMonomer ) ; } if ( fieldName != null ) { switch ( fieldName ) { case "monomerID" : parser . nextToken ( ) ; currentMonomer . setMonomerID ( parser . getText ( ) ) ; break ; case "monomerName" : parser . nextToken ( ) ; currentMonomer . setMonomerName ( parser . getText ( ) ) ; break ; case "naturalAnalogon" : parser . nextToken ( ) ; currentMonomer . setNaturalAnalogon ( parser . getText ( ) ) ; break ; case "monomerType" : parser . nextToken ( ) ; currentMonomer . setMonomerType ( parser . getText ( ) ) ; break ; case "polymerType" : parser . nextToken ( ) ; currentMonomer . setPolymerType ( parser . getText ( ) ) ; break ; case "category" : parser . nextToken ( ) ; currentMonomer . setCategory ( parser . getText ( ) ) ; break ; case "shape" : parser . nextToken ( ) ; currentMonomer . setShape ( parser . getText ( ) ) ; break ; case "fontColor" : parser . nextToken ( ) ; currentMonomer . setFontColor ( parser . getText ( ) ) ; break ; case "backgroundColor" : parser . nextToken ( ) ; currentMonomer . setBackgroundColor ( parser . getText ( ) ) ; break ; default : break ; } } parser . nextToken ( ) ; } return config ; } | Private routine to deserialize JSON containing monomer categorization data . This is done manually to give more freedom regarding data returned by the webservice . |
18,063 | 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 . setCapGroupName ( attachment . getChildText ( CAP_GROUP_NAME_ELEMENT , ns ) ) ; att . setCapGroupSMILES ( attachment . getChildText ( CAP_GROUP_SMILES_ELEMENT , ns ) ) ; return att ; } | Convert ATTACHMENT element to Attachment object |
18,064 | 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 . getChildren ( ) . add ( e ) ; } if ( null != att . getLabel ( ) && att . getLabel ( ) . length ( ) > 0 ) { Element e = new Element ( ATTACHEMENT_LABEL_ELEMENT ) ; e . setText ( att . getLabel ( ) ) ; attachment . getChildren ( ) . add ( e ) ; } if ( null != att . getCapGroupName ( ) && att . getCapGroupName ( ) . length ( ) > 0 ) { Element e = new Element ( CAP_GROUP_NAME_ELEMENT ) ; e . setText ( att . getCapGroupName ( ) ) ; attachment . getChildren ( ) . add ( e ) ; } if ( null != att . getCapGroupSMILES ( ) && att . getCapGroupSMILES ( ) . length ( ) > 0 ) { Element e = new Element ( CAP_GROUP_SMILES_ELEMENT ) ; e . setText ( att . getCapGroupSMILES ( ) ) ; attachment . getChildren ( ) . add ( e ) ; } return attachment ; } | This method converts Attachment to ATTACHMENT XML element |
18,065 | 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 . getCapGroupSMILES ( ) ; if ( null != smiles ) { if ( ! Chemistry . getInstance ( ) . getManipulator ( ) . validateSMILES ( smiles ) ) { throw new MonomerException ( "Attachment cap group SMILES is invalid" ) ; } List < String > labels = getAttachmentLabels ( smiles ) ; if ( null == labels || labels . size ( ) != 1 ) { throw new MonomerException ( "Attachment must have one R group in SMILES" ) ; } if ( ! ( labels . get ( 0 ) . equals ( attachment . getLabel ( ) ) ) ) { throw new MonomerException ( "R group in monomer SMILES and R group label must match" ) ; } } return true ; } | 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 |
18,066 | 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 encodedMolfile = monomer . getChildText ( MONOMER_MOL_FILE_ELEMENT , ns ) ; String molfile = null ; try { molfile = MolfileEncoder . decode ( encodedMolfile ) ; } catch ( EncoderException ex ) { throw new MonomerException ( "Invalid monomer molfile" ) ; } m . setMolfile ( molfile ) ; m . setMonomerType ( monomer . getChildText ( MONOMER_TYPE_ELEMENT , ns ) ) ; m . setPolymerType ( monomer . getChildText ( POLYMER_TYPE_ELEMENT , ns ) ) ; m . setNaturalAnalog ( monomer . getChildText ( NATURAL_ANALOG_ELEMENT , ns ) ) ; m . setName ( monomer . getChildText ( MONOMER_NAME_ELEMENT , ns ) ) ; Element attachmentElement = monomer . getChild ( ATTACHEMENTS_ELEMENT , ns ) ; if ( null != attachmentElement ) { List attachments = attachmentElement . getChildren ( ATTACHEMENT_ELEMENT , ns ) ; List < Attachment > l = new ArrayList < Attachment > ( ) ; Iterator i = attachments . iterator ( ) ; while ( i . hasNext ( ) ) { Element attachment = ( Element ) i . next ( ) ; Attachment att = getAttachment ( attachment ) ; l . add ( att ) ; } m . setAttachmentList ( l ) ; } return m ; } | Convert monomer element to Monomer object |
18,067 | 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 ) ; } if ( null != monomer . getCanSMILES ( ) ) { Element e = new Element ( MONOMER_SMILES_ELEMENT ) ; e . setText ( monomer . getCanSMILES ( ) ) ; element . getChildren ( ) . add ( e ) ; } if ( null != monomer . getMolfile ( ) ) { Element e = new Element ( MONOMER_MOL_FILE_ELEMENT ) ; String encodedMolfile = null ; try { encodedMolfile = MolfileEncoder . encode ( monomer . getMolfile ( ) ) ; } catch ( EncoderException ex ) { throw new MonomerException ( "Invalid monomer molfile" ) ; } e . setText ( encodedMolfile ) ; element . getChildren ( ) . add ( e ) ; } if ( null != monomer . getMonomerType ( ) ) { Element e = new Element ( MONOMER_TYPE_ELEMENT ) ; e . setText ( monomer . getMonomerType ( ) ) ; element . getChildren ( ) . add ( e ) ; } if ( null != monomer . getPolymerType ( ) ) { Element e = new Element ( POLYMER_TYPE_ELEMENT ) ; e . setText ( monomer . getPolymerType ( ) ) ; element . getChildren ( ) . add ( e ) ; } if ( null != monomer . getNaturalAnalog ( ) ) { Element e = new Element ( NATURAL_ANALOG_ELEMENT ) ; e . setText ( monomer . getNaturalAnalog ( ) ) ; element . getChildren ( ) . add ( e ) ; } if ( null != monomer . getName ( ) ) { Element e = new Element ( MONOMER_NAME_ELEMENT ) ; e . setText ( monomer . getName ( ) ) ; element . getChildren ( ) . add ( e ) ; } List < Attachment > l = monomer . getAttachmentList ( ) ; if ( null != l && l . size ( ) > 0 ) { Element attachments = new Element ( ATTACHEMENTS_ELEMENT ) ; for ( int i = 0 ; i < l . size ( ) ; i ++ ) { Attachment att = l . get ( i ) ; Element attachment = getAttachementElement ( att ) ; attachments . getChildren ( ) . add ( attachment ) ; } element . getChildren ( ) . add ( attachments ) ; } return element ; } | This method converts Monomer to MONOMER XML element |
18,068 | 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 . size ( ) ) { return true ; } else { return false ; } } | This method checks if strings in a list are unique |
18,069 | 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 |
18,070 | 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 . MoleculeInfo info = Chemistry . getInstance ( ) . getManipulator ( ) . getMoleculeInfo ( Chemistry . getInstance ( ) . getManipulator ( ) . getMolecule ( capSmi , null ) ) ; MoleculeProperty moleculeinfo = new MoleculeProperty ( ) ; moleculeinfo . setExactMass ( info . getExactMass ( ) ) ; moleculeinfo . setMolecularFormula ( info . getMolecularFormula ( ) ) ; moleculeinfo . setMolecularWeight ( info . getMolecularWeight ( ) ) ; return moleculeinfo ; } } return null ; } | This method returns the MoleculeInfo for the input R group label of this monomer |
18,071 | 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 |
18,072 | public static JKCacheManager getCacheManager ( ) { if ( JKCacheFactory . defaultCacheManager == null ) { logger . debug ( "init cacheManager" ) ; defaultCacheManager = new JKDefaultCacheManager ( ) ; } return JKCacheFactory . defaultCacheManager ; } | Gets the default cache manager . |
18,073 | 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 . |
18,074 | 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 . |
18,075 | 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 . |
18,076 | 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 . |
18,077 | public void addJKTableColumn ( String keyLabel ) { JKTableColumn col = new JKTableColumn ( ) ; col . setName ( keyLabel ) ; addJKTableColumn ( col ) ; } | Adds the JK table column . |
18,078 | public void insertConstructor ( InsertableConstructor insertableConstructor ) throws CannotCompileException , AfterBurnerImpossibleException , NotFoundException { List < CtConstructor > constructorList = extractExistingConstructors ( insertableConstructor ) ; log . info ( "constructor : " + constructorList . toString ( ) ) ; if ( ! constructorList . isEmpty ( ) ) { for ( CtConstructor constructor : constructorList ) { constructor . insertBeforeBody ( insertableConstructor . getConstructorBody ( constructor . getParameterTypes ( ) ) ) ; } } else { throw new AfterBurnerImpossibleException ( "No suitable constructor was found in class " + insertableConstructor . getClassToInsertInto ( ) . getName ( ) + ". Add a constructor that is accepted by the InsertableConstructor. Don't use non static inner classes." ) ; } } | Inserts java instructions into all constructors a given class . |
18,079 | protected ValidationResult getCachedResult ( String certFingerprint ) { CachedValidationResult cvr = validationResultsCache . get ( certFingerprint ) ; if ( cvr == null ) return null ; if ( ! cachedValidationResultHasExpired ( cvr , System . currentTimeMillis ( ) ) ) { return cvr . getResult ( ) ; } validationResultsCache . remove ( certFingerprint , cvr ) ; return null ; } | Gets a validation result from the memory cache |
18,080 | 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 fingerprint for " + "certificate: %s. Cause: %s" , CertificateUtils . format ( certChain [ 0 ] , FormatMode . COMPACT_ONE_LINE ) , t . getMessage ( ) ) ; throw new VOMSError ( errorMsg , t ) ; } ValidationResult res = getCachedResult ( certFingerprint ) ; if ( res == null ) { res = validator . validate ( certChain ) ; validationResultsCache . putIfAbsent ( certFingerprint , new CachedValidationResult ( certFingerprint , res ) ) ; } return res ; } | Validates a certificate chain using the wrapped validator caching the result for future validation calls . |
18,081 | 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 . |
18,082 | 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 . |
18,083 | public JsTopicControls getJsTopicControlsFromProxyClass ( Class < ? > proxy ) { Class < ? > realClass = unProxyClassServices . getRealClass ( proxy ) ; return realClass . getAnnotation ( JsTopicControls . class ) ; } | get JsTopicControls from JsTopicAccessController instance |
18,084 | 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 ; } else { logger . debug ( "Read '{}' option in web.xml : '{}'." , Constants . Options . STACKTRACE_LENGTH , stacktrace ) ; } } else { stacktrace = ocelotConfigurationsStack . get ( ) ; logger . debug ( "Read '{}' option from producer : '{}'." , Constants . Options . STACKTRACE_LENGTH , stacktrace ) ; } int stacktracelenght = Integer . parseInt ( stacktrace ) ; logger . debug ( "'{}' value : '{}'." , Constants . Options . STACKTRACE_LENGTH , stacktracelenght ) ; setStacktracelength ( stacktracelenght ) ; } | Read in web . xml the optional STACKTRACE_LENGTH config and set it in StacktraceConfigurationManager |
18,085 | 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 ( port ) . append ( "/rest" ) ; return basePath . toString ( ) ; } | Generate the base path for the retina . |
18,086 | 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 ) { Object result = getResult ( jsonArg , argumentServices . getIJsonMarshallerInstance ( juma . value ( ) ) , juma . type ( ) ) ; argumentServices . checkType ( result , paramType ) ; return result ; } else { return convertArgument ( jsonArg , paramType ) ; } } | Convert json to Java |
18,087 | JsonUnmarshaller getJsonUnmarshallerAnnotation ( Annotation [ ] annotations ) { for ( Annotation annotation : annotations ) { if ( JsonUnmarshaller . class . isInstance ( annotation ) ) { return ( JsonUnmarshaller ) annotation ; } } return null ; } | return the JsonUnmarshaller annotation |
18,088 | 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 |
18,089 | 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 ( ParameterizedType . class . isInstance ( paramType ) ) { JavaType javaType = getJavaType ( paramType ) ; logger . debug ( "Try to convert '{}' to JavaType : '{}'", rg, aramType) ;
result = getObjectMapper ( ) . readValue ( arg , javaType ) ; logger . debug ( "Conversion of '{}' to '{}' : OK", rg, aramType) ;
} else if ( Class . class . isInstance ( paramType ) ) { Class cls = ( Class ) paramType ; logger . debug ( "Try to convert '{}' to Class '{}'" , arg , paramType ) ; checkStringArgument ( cls , arg ) ; result = getObjectMapper ( ) . readValue ( arg , cls ) ; logger . debug ( "Conversion of '{}' to '{}' : OK", rg, aramType) ;
} else { logger . warn ( "Conversion of '{}' to '{}' not yet supported", rg, aramType) ;
} } catch ( IOException ex ) { logger . debug ( "Conversion of '{}' to '{}' failed" , arg , paramType ) ; throw new IllegalArgumentException ( paramType . toString ( ) ) ; } return result ; } | try to convert json argument in java type |
18,090 | 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 |
18,091 | 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" ) ) ; logMetric ( metric ) ; String inputText = "Gustav Klimt (July 14, 1862 – February 6, 1918) was an Austrian symbolist painter and one " + "of the most prominent members of the Vienna Secession movement. Klimt is noted for his paintings, " + "murals, sketches, and other objets d'art. Klimt's primary subject was the female body;[1] " + "his works are marked by a frank eroticism.[2]" ; metric = compareApiInstance . compare ( new Term ( "painter" ) , new Text ( inputText ) ) ; logMetric ( metric ) ; LOG . info ( "Compare API: compareBulk" ) ; CompareModels toCompare1 = new CompareModels ( new Term ( "apple" ) , new Term ( "banana" ) ) ; CompareModels toCompare2 = new CompareModels ( new Term ( "banana" ) , new Term ( "fruit" ) ) ; CompareModels toCompare3 = new CompareModels ( new Term ( "apple" ) , new Term ( "orange" ) ) ; CompareModels [ ] toCompareBulk = { toCompare1 , toCompare2 , toCompare3 } ; Metric [ ] metrics = compareApiInstance . compareBulk ( toCompareBulk ) ; for ( Metric metricFromBulk : metrics ) { logMetric ( metricFromBulk ) ; } } | The Compare API usage . |
18,092 | 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 ) { throw new IllegalStateException ( "A image stream cannot be received." ) ; } } LOG . info ( "Image API: getOverlayImage" ) ; try ( ByteArrayInputStream inputStream = api . compare ( TEXT_1 , TEXT_2 ) ) { if ( inputStream . read ( ) == 0 ) { throw new IllegalStateException ( "A image stream cannot be received." ) ; } } LOG . info ( "Image API: getImageForBulkExpressions" ) ; List < Image > images = api . getImageBulk ( TEXT_1 , TERM_1 ) ; for ( Image image : images ) { LOG . info ( "Image: imageData size: " + image . getImageData ( ) . length ) ; } } | The Image API usage . |
18,093 | 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: " + retina . getRetinaName ( ) + " Description: " + retina . getRetinaDescription ( ) + " Terms in the retina: " + retina . getNumberOfTermsInRetina ( ) ) ; } Retina retina = api . retinaByName ( RETINA_NAME ) ; LOG . info ( "Retina: Name: " + retina . getRetinaName ( ) + " Description: " + retina . getRetinaDescription ( ) + " Terms in the retina: " + retina . getNumberOfTermsInRetina ( ) ) ; } | The Retinas API usage . |
18,094 | 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 . getContexts ( "apple" , new Pagination ( 0 , 2 ) , true ) ; logContext ( contexts ) ; List < Term > terms ; LOG . info ( "Terms API: getSimilarTerms" ) ; terms = api . getSimilarTerms ( "tiger" ) ; logTerms ( terms ) ; terms = api . getSimilarTerms ( "tiger" , null , PosType . NOUN ) ; logTerms ( terms ) ; terms = api . getSimilarTerms ( "tiger" , null , PosType . NOUN , true ) ; logTerms ( terms ) ; LOG . info ( "Terms API: getTerm" ) ; terms = api . getTerm ( "apple" ) ; logTerms ( terms ) ; System . out . println ( ) ; terms = api . getTerm ( "banana" , new Pagination ( 0 , 2 ) , true ) ; logTerms ( terms ) ; System . out . println ( ) ; LOG . info ( "Terms API: getTerm NULL TEST" ) ; terms = api . getTerm ( null ) ; logTerms ( terms ) ; } | The Terms API usage . |
18,095 | 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, Linux, and Mac servers, but you can defend against it." ; String text3 = "However, Shellshock is not as bad as HeartBleed. Not yet, anyway." ; LOG . info ( "The Text API usage." ) ; Texts api = retinaApisInstance . textApi ( ) ; LOG . info ( "Text API: getKeywordsForText" ) ; List < String > keywords = api . getKeywords ( text ) ; logKeywords ( keywords ) ; LOG . info ( "Text API: getRepresentationForText" ) ; List < Fingerprint > fingerprints = api . getFingerprints ( text2 ) ; logFingerprints ( fingerprints ) ; LOG . info ( "Text API: getRepresentationsForBulkText" ) ; fingerprints = api . getFingerprintBulk ( 0.1 , TEXT_1 , TEXT_2 ) ; logFingerprints ( fingerprints ) ; LOG . info ( "Text API: getSlicesForText" ) ; List < Text > texts = api . getSlices ( text ) ; logTexts ( texts ) ; texts = api . getSlices ( text3 , new Pagination ( 0 , 2 ) , true ) ; logTexts ( texts ) ; LOG . info ( "Text API: getTokensForText" ) ; List < String > tokens = api . getTokens ( text2 , new PosTag [ ] { PosTag . CC , PosTag . LRB } ) ; logTokens ( tokens ) ; tokens = api . getTokens ( text2 , new PosTag [ ] { } ) ; logTokens ( tokens ) ; } | The Text API usage . |
18,096 | 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 { doEvents ( - 1 ) ; } } } | Consume events until interrupted |
18,097 | 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 ( field ) ) { throw new NoSuchElementException ( "Field " + field + " not valid in this extension" ) ; } return extensionFieldType . fromString ( fields . get ( field ) . value ) ; } | Return the value for the field with a given name and type . |
18,098 | 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 . getRuntimeClasspathElements ( ) . iterator ( ) ; i . hasNext ( ) ; ) { String fileName = ( String ) i . next ( ) ; try { results . add ( new File ( fileName ) . getCanonicalPath ( ) ) ; } catch ( IOException e ) { throw new RuntimeException ( "Classpath element not found: " + fileName , e ) ; } } } if ( includes . contains ( CLASSPATH_INCLUDE_ALL ) || includes . contains ( CLASSPATH_INCLUDE_ARTIFACTS ) ) { for ( Iterator i = project . getArtifacts ( ) . iterator ( ) ; i . hasNext ( ) ; ) { Artifact artifact = ( Artifact ) i . next ( ) ; if ( artifact . getType ( ) . equals ( "jar" ) && artifact . getClassifier ( ) == null ) { try { results . add ( artifact . getFile ( ) . getCanonicalPath ( ) ) ; } catch ( IOException e ) { throw new RuntimeException ( "Maven artifact file not found: " + artifact , e ) ; } } } } if ( includes . contains ( CLASSPATH_INCLUDE_ALL ) || includes . contains ( CLASSPATH_INCLUDE_PLUGINS ) ) { for ( Iterator i = pluginArtifacts . iterator ( ) ; i . hasNext ( ) ; ) { Artifact artifact = ( Artifact ) i . next ( ) ; if ( artifact . getType ( ) . equals ( "jar" ) && artifact . getClassifier ( ) == null ) { try { results . add ( artifact . getFile ( ) . getCanonicalPath ( ) ) ; } catch ( IOException e ) { throw new RuntimeException ( "Maven plugin-artifact file not found: " + artifact , e ) ; } } } } return new ArrayList ( results ) ; } | 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 artifacts . |
18,099 | 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 ( ) ; ) { String key = ( String ) iter . next ( ) ; Provider provider ; try { provider = ( Provider ) getContainer ( ) . lookup ( Provider . class . getName ( ) , key ) ; } catch ( Exception e ) { log . warn ( "Failed to lookup provider for key: {}" , key , e ) ; continue ; } if ( provider != null ) { if ( found == null ) { found = new HashMap ( ) ; } found . put ( key , provider ) ; } } return found ; } | Find any providers which are available in the container . |
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