idx int64 0 165k | question stringlengths 73 5.81k | target stringlengths 5 918 |
|---|---|---|
141,500 | public String generateNaturalAnalogSequenceRNA ( String notation ) throws org . helm . notation2 . parser . exceptionparser . NotationException , HELM2HandledException , ValidationException , MonomerLoadingException , ChemistryException { String result = SequenceConverter . getNucleotideNaturalAnalogSequenceFromNotatio... | method to generate the natural analogue sequence for all rna - sequences from an HELM input |
141,501 | public String convertMolFileSMILESWithAtomMapping ( String molfile , List < Attachment > attachments ) throws CTKException , ChemistryException { return SMILES . convertMolToSMILESWithAtomMapping ( molfile , attachments ) ; } | method to generate a smiles with atom mapping for a given molfile with the given attachments |
141,502 | public static List < MonomerNotation > getListOfMonomerNotation ( List < PolymerNotation > polymers ) { List < MonomerNotation > items = new ArrayList < MonomerNotation > ( ) ; for ( PolymerNotation polymer : polymers ) { items . addAll ( polymer . getListMonomers ( ) ) ; } return items ; } | method to get all MonomerNotations for all given polymers |
141,503 | public static List < Monomer > getListOfMonomer ( List < MonomerNotation > monomerNotations ) throws MonomerException , HELM2HandledException , CTKException , NotationException , ChemistryException , MonomerLoadingException { List < Monomer > items = new ArrayList < Monomer > ( ) ; for ( int i = 0 ; i < monomerNotation... | method to get all monomers for all MonomerNotations |
141,504 | public static Monomer getMonomer ( String type , String id , String info ) throws MonomerException , NotationException , ChemistryException { try { if ( id . startsWith ( "[" ) && id . endsWith ( "]" ) ) { id = id . substring ( 1 , id . length ( ) - 1 ) ; } MonomerFactory monomerFactory = MonomerFactory . getInstance (... | method to get the monomer from the database! |
141,505 | public static JKLocale valueOf ( final String localeString ) { return localeString . equals ( ARABIC . shortName ) ? ARABIC : ENGLISH ; } | Value of . |
141,506 | public String getAuditText ( ) { final StringBuffer b = new StringBuffer ( ) ; b . append ( getOldValue ( ) . replaceAll ( "," , "\n" ) ) ; b . append ( "-----------------------------------------\n" ) ; b . append ( getNewValue ( ) . replaceAll ( "," , "\n" ) ) ; b . append ( "-----------------------------------------\... | Gets the audit text . |
141,507 | public float calculate ( HELM2Notation helm2notation , int unitType ) throws ExtinctionCoefficientException , ChemistryException { LOG . debug ( "ExtinctionCalculation is starting with the unitType: " + unitType ) ; float result = 0.0f ; List < PolymerNotation > polymerNodes = helm2notation . getListOfPolymers ( ) ; fo... | method to calculate the extinction coefficient for the whole HELM molecule |
141,508 | private static float calculateExtinctionFromRNA ( List < Monomer > monomers ) throws CalculationException , IOException { LOG . debug ( "ExtinctionCalculation of RNA" ) ; float resultSingle = 0.0f ; float resultDi = 0.0f ; String previous = "" ; if ( monomers . size ( ) == 0 ) { throw new CalculationException ( "Input ... | method to calculate the extinction coefficient for rna |
141,509 | private static float calculateExtinctionFromPeptide ( List < Monomer > monomers ) throws IOException , HELM2HandledException { if ( null == monomers || monomers . isEmpty ( ) ) { return 0.0f ; } Map < String , Integer > countMap = new HashMap < String , Integer > ( ) ; for ( Monomer monomer : monomers ) { if ( aminoAci... | method to calculate the extinction coefficient for peptide |
141,510 | public static boolean isAuthenticed ( String host , int port , String userName , String password ) throws NamingException { log . info ( "isAuthenticed" ) ; Hashtable < String , String > env = new Hashtable < String , String > ( ) ; env . put ( Context . INITIAL_CONTEXT_FACTORY , "com.sun.jndi.ldap.LdapCtxFactory" ) ; ... | Checks if is authenticed . |
141,511 | protected static String fixKey ( final String key ) { if ( key . startsWith ( getKeyPrefix ( ) ) ) { return key ; } return getKeyPrefix ( ) + "-" + key ; } | Fix key . |
141,512 | public static float getFloat ( final String key , final float def ) { try { return systemRoot . getFloat ( fixKey ( key ) , def ) ; } catch ( final Exception e ) { return def ; } } | Gets the float . |
141,513 | public static Hashtable < String , String > getHashtable ( final String name ) { final Hashtable < String , String > hash = new Hashtable < String , String > ( ) ; try { final String configStr = UserPreferences . get ( fixKey ( name ) , "" ) ; if ( ! configStr . equals ( "" ) ) { final String [ ] rows = configStr . spl... | Gets the hashtable . |
141,514 | public static int getInt ( final String key , final int def ) { try { return systemRoot . getInt ( fixKey ( key ) , def ) ; } catch ( final Exception e ) { return def ; } } | Gets the int . |
141,515 | public static void putHashTable ( final String name , final Hashtable hash ) { final Enumeration < String > keys = hash . keys ( ) ; final StringBuffer buf = new StringBuffer ( "" ) ; while ( keys . hasMoreElements ( ) ) { if ( ! buf . toString ( ) . equals ( "" ) ) { buf . append ( ";" ) ; } final String key = keys . ... | Put hash table . |
141,516 | public static void setKeyPrefix ( final String keyPrefix ) { UserPreferences . keyPrefix = keyPrefix ; try { systemRoot . sync ( ) ; } catch ( final Exception e ) { JKExceptionUtil . handle ( e ) ; } } | Sets the key prefix . |
141,517 | private static void initializeNucleotideTemplates ( ) throws NucleotideLoadingException { InputStream in = null ; File localFile = new File ( LOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATH ) ; Map < String , Map < String , String > > templates = null ; if ( localFile . exists ( ) ) { try { in = new FileInputStream ( localFile ) ;... | This method is called during startup use local version if exist otherwise use XML version in jar |
141,518 | public void saveNucleotideTemplates ( ) throws IOException { File f = new File ( NOTATION_DIRECTORY ) ; if ( ! f . exists ( ) ) { f . mkdir ( ) ; } String nucleotideTemplatesXML = NucleotideParser . getNucleotideTemplatesXML ( getNucleotideTemplates ( ) ) ; FileOutputStream fos = new FileOutputStream ( LOCAL_NUCLEOTIDE... | save Nucleotide Templates to disk file |
141,519 | @ SuppressWarnings ( "rawtypes" ) public Class [ ] getParamtersTypes ( ) { final Class [ ] types = new Class [ this . paramters . length ] ; for ( int i = 0 ; i < types . length ; i ++ ) { types [ i ] = this . paramters [ i ] . getClass ( ) ; } return types ; } | get the types of the parameters using java reflection . |
141,520 | private void readConfigFile ( ) { File configFile = new File ( CONFIG_FILE_PATH ) ; if ( ! configFile . exists ( ) ) { resetConfigToDefault ( ) ; } try { PropertiesConfiguration conf = new PropertiesConfiguration ( CONFIG_FILE_PATH ) ; chemistry = conf . getString ( CHEMISTRY_PLUGIN ) ; } catch ( ConfigurationException... | method to read the configuration file |
141,521 | public static boolean compileJavaClass ( String sourceCode ) { try { String fileName = getClassName ( sourceCode ) . concat ( ".java" ) ; logger . info ( "Compiling Java Class ({})" , fileName ) ; File rootDir = JKIOUtil . createTempDirectory ( ) ; String packageDir = getPackageDir ( sourceCode ) ; File sourceFile ; if... | Compile java class . |
141,522 | public void showAndChoose ( IConsumer < File > consumer ) { this . consumer = consumer ; initSrvNodeFile ( ) ; Intent activityTreeIntent = new Intent ( activity , ActivityTreeChooser . class ) ; activityTreeIntent . putExtra ( FragmentNodes . ARG_ID_NODE_SRVNODES , new String [ ] { idFolderStart , idSrvGetNodeFile , id... | You must provide fileFilter idFolderStart and title to invoke it! |
141,523 | public static String getHELMNotationString ( Element rootElement ) { Element helmNotationElement = rootElement . getChild ( "HelmNotation" ) ; return helmNotationElement . getText ( ) ; } | Extracts the HELM string from the root node of the XHELM document |
141,524 | public static String getComplexNotationString ( Element rootElement ) { Element helmNotationElement = rootElement . getChild ( "HelmNotation" ) ; return helmNotationElement . getText ( ) ; } | Extracts the complex notation string from the root node of the XHELM document |
141,525 | public static MonomerStore getMonomerStore ( Element rootElement ) throws MonomerException , IOException { MonomerStore monomerStore = new MonomerStore ( ) ; Element monomerListElement = rootElement . getChild ( "Monomers" ) ; if ( monomerListElement != null ) { @ SuppressWarnings ( "unchecked" ) List < Element > eleme... | Generates the monomer store from a given XHELM document |
141,526 | public boolean isNumeric ( ) { final Class c = getColumnClass ( ) ; return c . equals ( Integer . class ) || c . equals ( Float . class ) || c . equals ( Long . class ) || c . equals ( BigDecimal . class ) ; } | Checks if is numeric . |
141,527 | public void setColumnClassName ( final String columnClassName ) throws ClassNotFoundException { if ( columnClassName . equals ( "byte[]" ) ) { setColumnClass ( Object . class ) ; } else { setColumnClass ( Class . forName ( columnClassName ) ) ; } this . columnClassName = columnClassName ; } | Sets the column class name . |
141,528 | public static String generateMDL ( final HELM2Notation helm2notation ) throws BuilderMoleculeException , CTKException , NotationException , ChemistryException { LOG . debug ( "Generate smiles representation for the whole HELM molecule" ) ; String smiles = SMILES . getSMILESForAll ( helm2notation ) ; LOG . debug ( "Conv... | method to generate MDL for a HELM molecule |
141,529 | public void callMethod ( final MethodCallInfo info ) { this . logger . info ( "calling remote method " . concat ( info . toString ( ) ) ) ; try ( Socket socket = new Socket ( this . host , this . port ) ) { final ObjectOutputStream out = new ObjectOutputStream ( socket . getOutputStream ( ) ) ; out . writeObject ( info... | Call the remote method based on the passed MethodCallInfo parameter . |
141,530 | protected static Vector convertToVector ( final Object [ ] anArray ) { if ( anArray == null ) { return null ; } final Vector v = new Vector ( anArray . length ) ; for ( final Object element : anArray ) { v . addElement ( element ) ; } return v ; } | Returns a vector that contains the same objects as the array . |
141,531 | private static Vector newVector ( final int size ) { final Vector v = new Vector ( size ) ; v . setSize ( size ) ; return v ; } | New vector . |
141,532 | public String getColumnName ( final int column ) { Object id = null ; if ( column < this . columnIdentifiers . size ( ) && column >= 0 ) { id = this . columnIdentifiers . elementAt ( column ) ; } return id == null ? super . getColumnName ( column ) : id . toString ( ) ; } | Returns the column name . |
141,533 | private void justifyRows ( final int from , final int to ) { this . dataVector . setSize ( getRowCount ( ) ) ; for ( int i = from ; i < to ; i ++ ) { if ( this . dataVector . elementAt ( i ) == null ) { this . dataVector . setElementAt ( new Vector ( ) , i ) ; } } } | Justify rows . |
141,534 | public static String findPathJar ( final Class clas ) throws IllegalStateException { URL url ; String extURL ; try { url = clas . getProtectionDomain ( ) . getCodeSource ( ) . getLocation ( ) ; } catch ( final SecurityException ex ) { url = clas . getResource ( clas . getSimpleName ( ) + ".class" ) ; } extURL = url . t... | If the provided class has been loaded from a jar file that is on the local file system will find the absolute path to that jar file . |
141,535 | public static byte [ ] readStream ( final InputStream inStream ) { try { return IOUtils . toByteArray ( inStream ) ; } catch ( IOException e ) { throw new JKException ( e ) ; } } | Read stream . |
141,536 | public static String convertToString ( InputStream input ) throws IOException { try { if ( input == null ) { throw new IOException ( "Input Stream Cannot be NULL" ) ; } StringBuilder sb1 = new StringBuilder ( ) ; String line ; try { BufferedReader r1 = new BufferedReader ( new InputStreamReader ( input , "UTF-8" ) ) ; ... | Convert to string . |
141,537 | public static Reader getReader ( String name ) { InputStream inputStream = getInputStream ( name ) ; if ( inputStream != null ) { BufferedReader reader = new BufferedReader ( new InputStreamReader ( inputStream ) ) ; return reader ; } return null ; } | Gets the reader . |
141,538 | public static String getExtension ( final String fileName , final boolean withPoint ) { final int lastIndexOf = fileName . lastIndexOf ( "." ) ; if ( ! withPoint ) { return fileName . substring ( lastIndexOf + 1 ) ; } return fileName . substring ( lastIndexOf ) ; } | Gets the extension . |
141,539 | public static String removeExtension ( String fileName ) { final String separator = FILE_SEPARATOR ; String filename ; final int lastSeparatorIndex = fileName . lastIndexOf ( separator ) ; if ( lastSeparatorIndex == - 1 ) { filename = fileName ; } else { filename = fileName . substring ( lastSeparatorIndex + 1 ) ; } fi... | Removes the extension . |
141,540 | public static File writeDataToFile ( final byte [ ] data , final File file , final boolean append ) { try ( FileOutputStream out = new FileOutputStream ( file , append ) ) { out . write ( data ) ; out . flush ( ) ; out . close ( ) ; return file ; } catch ( Exception e ) { JKExceptionUtil . handle ( e ) ; return null ; ... | Write data to file . |
141,541 | public static Properties readPropertiesStream ( InputStream inputStream ) { try { final Properties prop = new Properties ( ) ; prop . load ( new InputStreamReader ( inputStream , Charset . forName ( "utf-8" ) ) ) ; JKCollectionUtil . fixPropertiesKeys ( prop ) ; return prop ; } catch ( IOException e ) { JKExceptionUtil... | Read properties stream . |
141,542 | public static File writeFileToTempDirectory ( final byte [ ] data , final String fileName ) { try { File file = createTempDirectory ( ) ; File out = new File ( file , fileName ) ; out . deleteOnExit ( ) ; file . deleteOnExit ( ) ; return writeDataToFile ( data , out ) ; } catch ( IOException e ) { JKExceptionUtil . han... | Write file to temp directory . |
141,543 | public static File createTempFile ( final String ext ) { try { File file ; file = File . createTempFile ( "jk-" , "." + ext ) ; return file ; } catch ( IOException e ) { JK . throww ( e ) ; return null ; } } | Creates the temp file . |
141,544 | public static Process executeFile ( final String fileName ) { try { final String command = "cmd /c \"" + fileName + "\"" ; logger . info ( command ) ; return Runtime . getRuntime ( ) . exec ( command ) ; } catch ( IOException e ) { throw new RuntimeException ( e ) ; } } | Execute file . |
141,545 | public static String getSqlFile ( String fileName ) { String file = "/jk/sql/" . concat ( fileName ) ; logger . debug ( "Loading sql file: " , file ) ; return readFile ( file ) ; } | Gets the sql file . |
141,546 | public static void clearTempFiles ( ) { String userFolderPath = getUserFolderPath ( false ) ; File file = new File ( userFolderPath ) ; deleteDir ( file ) ; } | Clear temp files . |
141,547 | public static void startFakeThread ( ServerSocket server ) { Thread thread = new Thread ( new FakeRunnable ( server ) ) ; thread . start ( ) ; } | Start fake thread . |
141,548 | public static String getReportsOutPath ( boolean appendFileSeprator ) { String userLocalPath = getUserFolderPath ( true ) ; String reportPath = userLocalPath + REPORTS_OUT_PATH ; checkFolderPath ( reportPath , true ) ; if ( appendFileSeprator ) { reportPath += FILE_SEPARATOR ; } return reportPath ; } | Gets the reports out path . |
141,549 | public static List < String > getFilesInFolder ( String folder , String ext ) { List < String > files = new Vector < > ( ) ; File dir = new File ( folder ) ; if ( dir . exists ( ) && dir . isDirectory ( ) ) { String [ ] list = dir . list ( ) ; for ( String file : list ) { if ( file . endsWith ( ext ) ) { files . add ( ... | Gets the files in folder . |
141,550 | public static void copResourcesFromJarToDir ( String sourceClassPath , File dest ) { try { List < File > resourcesInnPackage = getResourcesInnPackage ( sourceClassPath ) ; for ( File file : resourcesInnPackage ) { JK . printBlock ( "Copying file: " + file . getName ( ) + " to folder " + dest . getAbsolutePath ( ) ) ; F... | Cop resources from jar to dir . |
141,551 | public static List < File > getResourcesInnPackage ( String root ) { try { logger . debug ( "getResourcesInnPackage for package: " + root ) ; ClassLoader loader = Thread . currentThread ( ) . getContextClassLoader ( ) ; URL url = loader . getResource ( root ) ; if ( url != null ) { logger . debug ( " URL :" + url . to... | Gets the resources inn package . |
141,552 | public static JKConfig readConfigFile ( String configFileName ) { URL url = getURL ( configFileName ) ; logger . debug ( configFileName + " Url is " , url . toString ( ) ) ; JKConfig config = new JKConfig ( url ) ; return config ; } | Read config file . |
141,553 | private static String convertLessThanOneThousand ( int number ) { String soFar ; if ( number % 100 < 20 ) { soFar = numNames [ number % 100 ] ; number /= 100 ; } else { soFar = numNames [ number % 10 ] ; number /= 10 ; soFar = tensNames [ number % 10 ] + soFar ; number /= 10 ; } if ( number == 0 ) { return soFar ; } re... | Convert less than one thousand . |
141,554 | public static double addAmounts ( final double num1 , final double num2 ) { final BigDecimal b1 = new BigDecimal ( num1 ) ; final BigDecimal b2 = new BigDecimal ( num2 ) ; BigDecimal b3 = b1 . add ( b2 ) ; b3 = b3 . setScale ( 3 , BigDecimal . ROUND_HALF_UP ) ; final double result = b3 . doubleValue ( ) ; return result... | Adds the amounts . |
141,555 | public static double fixAmount ( final double value ) { final BigDecimal b1 = new BigDecimal ( value ) ; final BigDecimal b2 = b1 . setScale ( 3 , BigDecimal . ROUND_HALF_UP ) ; return b2 . doubleValue ( ) ; } | Fix amount . |
141,556 | public static double subAmounts ( final double n1 , final double n2 ) { final BigDecimal b1 = new BigDecimal ( n1 ) ; final BigDecimal b2 = new BigDecimal ( n2 ) ; BigDecimal b3 = b1 . subtract ( b2 ) ; b3 = b3 . setScale ( 3 , BigDecimal . ROUND_HALF_UP ) ; final double result = b3 . doubleValue ( ) ; return result ; ... | Sub amounts . |
141,557 | public void fillEmail ( final MultiPartEmail email ) throws EmailException , IOException { email . setHostName ( getHost ( ) ) ; email . setSmtpPort ( getSmtpPort ( ) ) ; email . addTo ( getTo ( ) ) ; email . setFrom ( getFrom ( ) ) ; email . setSubject ( getSubject ( ) ) ; email . setMsg ( getMsg ( ) ) ; email . setSS... | Fill email . |
141,558 | public static Date toDate ( final Object value ) { if ( value instanceof Date ) { return ( Date ) value ; } if ( value == null || value . equals ( "null" ) ) { return null ; } if ( value instanceof String ) { throw new IllegalStateException ( "fix me" ) ; } return null ; } | To date . |
141,559 | public static float toFloat ( final Object value ) { if ( value instanceof Float ) { return ( float ) value ; } if ( value == null ) { return 0 ; } return new Float ( value . toString ( ) ) ; } | To float . |
141,560 | public static java . sql . Time toTime ( final Object value ) { if ( value == null ) { return null ; } if ( value instanceof java . sql . Time ) { return ( java . sql . Time ) value ; } if ( value instanceof java . util . Date ) { final Date date = ( java . util . Date ) value ; return new java . sql . Time ( date . ge... | To time . |
141,561 | public static boolean toBoolean ( Object value , boolean defaultValue ) { boolean result ; if ( value != null ) { if ( value instanceof Boolean ) { return ( ( Boolean ) value ) . booleanValue ( ) ; } if ( value . toString ( ) . trim ( ) . equals ( "1" ) || value . toString ( ) . trim ( ) . toLowerCase ( ) . equals ( "t... | To boolean . |
141,562 | public static double toDouble ( Object value , double defaultValue ) { if ( value == null || value . toString ( ) . trim ( ) . equals ( "" ) ) { return defaultValue ; } if ( value instanceof Double ) { return ( double ) value ; } if ( value instanceof Date ) { final Date date = ( Date ) value ; return date . getTime ( ... | To double . |
141,563 | public static int toInteger ( Object value , int defaultValue ) { if ( value == null || value . toString ( ) . trim ( ) . equals ( "" ) ) { return defaultValue ; } if ( value instanceof Integer ) { return ( Integer ) value ; } return ( int ) JKConversionUtil . toDouble ( value ) ; } | To integer . |
141,564 | public static void validateNotationObjects ( HELM2Notation helm2notation ) throws PolymerIDsException , MonomerException , GroupingNotationException , ConnectionNotationException , NotationException , ChemistryException , MonomerLoadingException , org . helm . notation2 . parser . exceptionparser . NotationException { ... | method to check if the generated notation objects by the parser are correct the polymer ids have to be unique ; all monomers have to be valid ; all used polymer ids in the grouping section have to be there ; all connections have to be valid |
141,565 | protected static boolean validateMonomers ( List < MonomerNotation > mon ) throws ChemistryException , MonomerLoadingException , org . helm . notation2 . parser . exceptionparser . NotationException { for ( MonomerNotation monomerNotation : mon ) { if ( ! ( isMonomerValid ( monomerNotation . getUnit ( ) , monomerNotati... | method to validate a list of MonomerNotation objects |
141,566 | private static boolean isConnectionSpecific ( ConnectionNotation connectionNotation ) { String connection = connectionNotation . getSourceUnit ( ) + ":" + connectionNotation . getrGroupSource ( ) + "-" + connectionNotation . getTargetUnit ( ) + ":" + connectionNotation . getrGroupTarget ( ) ; if ( connection . matches ... | method to check if the given connection is specific |
141,567 | private static List < Integer > getOccurencesOfMonomerNotation ( String sourceUnit , HELMEntity e , HELM2Notation helm2notation ) throws org . helm . notation2 . parser . exceptionparser . NotationException , AttachmentException { List < Integer > occurences = new ArrayList < Integer > ( ) ; try { occurences . add ( In... | method to get all occurences of the MonomerNotation |
141,568 | public static boolean validateGrouping ( HELM2Notation helm2notation ) { List < GroupingNotation > listGroupings = helm2notation . getListOfGroupings ( ) ; List < String > listPolymerIDs = helm2notation . getPolymerAndGroupingIDs ( ) ; for ( GroupingNotation grouping : listGroupings ) { for ( GroupingElement groupingEl... | method to validate every GroupNotation of the Notation objects |
141,569 | public static boolean validateUniquePolymerIDs ( HELM2Notation helm2notation ) { List < String > listPolymerIDs = helm2notation . getPolymerAndGroupingIDs ( ) ; Map < String , String > uniqueId = new HashMap < String , String > ( ) ; for ( String polymerID : listPolymerIDs ) { uniqueId . put ( polymerID , "" ) ; } if (... | method to check if all existent polymer ids are unique |
141,570 | private static void checkExistenceOfPolymerID ( String str , List < String > listPolymerIDs ) throws PolymerIDsException { if ( ! ( listPolymerIDs . contains ( str ) ) ) { LOG . info ( "Polymer Id does not exist" ) ; throw new PolymerIDsException ( "Polymer ID does not exist" ) ; } } | method to check if the given polymer id exists in the given list of polymer ids |
141,571 | private static boolean isMonomerValid ( String str , String type ) throws ChemistryException , MonomerLoadingException , org . helm . notation2 . parser . exceptionparser . NotationException { LOG . info ( "Is Monomer valid: " + str ) ; MonomerFactory monomerFactory = null ; monomerFactory = MonomerFactory . getInstanc... | method to check the monomer s validation |
141,572 | private static void checkPolymerIDSConnection ( ConnectionNotation not , List < String > listPolymerIDs ) throws PolymerIDsException { checkExistenceOfPolymerID ( not . getSourceId ( ) . getId ( ) , listPolymerIDs ) ; checkExistenceOfPolymerID ( not . getTargetId ( ) . getId ( ) , listPolymerIDs ) ; } | method to check for one connection if the two polymer ids exist |
141,573 | public static List < Monomer > getAllMonomers ( MonomerNotation not , int position ) throws HELM2HandledException , MonomerException , NotationException , ChemistryException , CTKException , MonomerLoadingException { List < Monomer > monomers = new ArrayList < Monomer > ( ) ; MonomerFactory monomerFactory = MonomerFact... | method to get for one MonomerNotation all valid contained monomers |
141,574 | public static List < Monomer > getAllMonomersOnlyBase ( MonomerNotation not ) throws HELM2HandledException , MonomerException , NotationException , ChemistryException , CTKException , MonomerLoadingException { LOG . debug ( "Get base for " + not ) ; List < Monomer > monomers = new ArrayList < Monomer > ( ) ; MonomerFac... | method to get for one MonomerNotation all valid contained monomers . But only the Base |
141,575 | private static void checkAttachmentPoint ( Monomer mon , String str ) throws AttachmentException { if ( ! ( mon . getAttachmentListString ( ) . contains ( str ) ) ) { if ( ! ( str . equals ( "?" ) || str . equals ( "pair" ) ) && ! mon . getAlternateId ( ) . equals ( "?" ) ) { LOG . info ( "Attachment point for source i... | method to check the attachment point s existence |
141,576 | private static boolean checkSingleAttachment ( List < Monomer > monomers , String rGroup , HELM2Notation helm2notation , ConnectionNotation not , InterConnections interconnection , String id ) throws AttachmentException { for ( Monomer monomer : monomers ) { checkAttachmentPoint ( monomer , rGroup ) ; String detail = n... | method to check for one attachment point the validation |
141,577 | private static List < Monomer > getMonomersRNA ( MonomerNotationUnitRNA rna , MonomerStore monomerStore , int position ) throws HELM2HandledException { try { List < Monomer > monomers = new ArrayList < Monomer > ( ) ; for ( int index = 0 ; index < rna . getContents ( ) . size ( ) ; index ++ ) { String id = rna . getCon... | method to get all monomers for MonomerNotationUnitRNA |
141,578 | private static List < Monomer > getMonomersRNAOnlyBase ( MonomerNotationUnitRNA rna , MonomerStore monomerStore ) throws HELM2HandledException { try { List < Monomer > monomers = new ArrayList < Monomer > ( ) ; for ( MonomerNotationUnit unit : rna . getContents ( ) ) { String id = unit . getUnit ( ) . replace ( "[" , "... | method to get only the nucleotide base for one MonomerNotationUnitRNA |
141,579 | private static void initComplementMap ( ) { complementMap = new HashMap < String , String > ( ) ; complementMap . put ( "A" , "U" ) ; complementMap . put ( "G" , "C" ) ; complementMap . put ( "C" , "G" ) ; complementMap . put ( "U" , "A" ) ; complementMap . put ( "T" , "A" ) ; complementMap . put ( "X" , "X" ) ; } | initialize Map to get the complement of each nucleotide |
141,580 | public static boolean areAntiparallel ( PolymerNotation polymerOne , PolymerNotation polymerTwo ) throws RNAUtilsException , HELM2HandledException , ChemistryException , NucleotideLoadingException { checkRNA ( polymerOne ) ; checkRNA ( polymerTwo ) ; PolymerNotation antiparallel = getAntiparallel ( polymerOne ) ; Strin... | method to check if two given polymers are complement to each other |
141,581 | public static String getMaxMatchFragment ( String seq1 , String seq2 ) throws NotationException { return getMaxMatchFragment ( seq1 , seq2 , MINUMUM_MATCH_FRAGMENT_LENGTH ) ; } | method to get the largest matched fragment between two sequences replace T with U before Match |
141,582 | public static String getMaxMatchFragment ( String seq1 , String seq2 , int minLength ) throws NotationException { if ( null == seq1 || null == seq2 ) { throw new NotationException ( "Both sequences must not be null " ) ; } if ( ! seq1 . equals ( seq1 . toUpperCase ( ) ) || ! seq2 . equals ( seq2 . toUpperCase ( ) ) ) {... | This method returns the largest matched fragment between two sequences replace T with U before match |
141,583 | public static void removeLastP ( PolymerNotation polymer ) throws RNAUtilsException , NotationException , HELM2HandledException { checkRNA ( polymer ) ; MonomerNotation lastObject = polymer . getPolymerElements ( ) . getListOfElements ( ) . get ( polymer . getPolymerElements ( ) . getListOfElements ( ) . size ( ) - 1 )... | method to remove the phosphate of the last nucleotide |
141,584 | public static void addLastP ( PolymerNotation polymer ) throws RNAUtilsException , NotationException , HELM2HandledException { checkRNA ( polymer ) ; MonomerNotation lastObject = polymer . getPolymerElements ( ) . getListOfElements ( ) . get ( polymer . getPolymerElements ( ) . getListOfElements ( ) . size ( ) - 1 ) ; ... | method to add a phosphate to the last polymer s nucleotide |
141,585 | public static PolymerNotation getInverse ( PolymerNotation polymer ) throws RNAUtilsException , org . helm . notation2 . exception . NotationException , ChemistryException , NucleotideLoadingException { checkRNA ( polymer ) ; PolymerNotation inverse ; try { inverse = SequenceConverter . readRNA ( generateInverse ( poly... | method to get the polymer with the inverse sequence of the current polymer |
141,586 | public static PolymerNotation getReverseComplement ( PolymerNotation polymer ) throws RNAUtilsException , org . helm . notation2 . exception . NotationException , ChemistryException , NucleotideLoadingException { checkRNA ( polymer ) ; PolymerNotation complementReversePolymer ; try { complementReversePolymer = Sequence... | method to get the polymer with the reverse complement sequence of the current polymer |
141,587 | private static StringBuilder generateInverse ( PolymerNotation polymer ) throws HELM2HandledException , RNAUtilsException , org . helm . notation2 . exception . NotationException , ChemistryException { initComplementMap ( ) ; String sequence = getNaturalAnalogSequence ( polymer ) ; StringBuilder sb = new StringBuilder ... | method to generate the inverse sequence of the given polymer |
141,588 | public static boolean hasNucleotideModification ( PolymerNotation polymer ) throws NotationException { for ( MonomerNotation current : polymer . getPolymerElements ( ) . getListOfElements ( ) ) { if ( hasModification ( current ) ) { return true ; } } return false ; } | method to check if the given PolymerNotation has a nucleotide Modification |
141,589 | private static boolean hasModification ( MonomerNotation monomerNotation ) throws NotationException { if ( monomerNotation instanceof MonomerNotationUnitRNA ) { if ( hasModification ( ( MonomerNotationUnitRNA ) monomerNotation ) ) { return true ; } } else if ( monomerNotation instanceof MonomerNotationGroup ) { for ( M... | method to check if the MonomerNotation contains a modification |
141,590 | private static boolean hasModification ( MonomerNotationUnitRNA monomerNotation ) { if ( monomerNotation . getUnit ( ) . contains ( "[" ) || monomerNotation . getUnit ( ) . contains ( "(X)" ) || monomerNotation . getUnit ( ) . endsWith ( ")" ) ) { return true ; } return false ; } | method to check if the MonomerNotationUnitRNA contains modification |
141,591 | public static List < ConnectionNotation > hybridizeAntiparallel ( PolymerNotation one , PolymerNotation two ) throws RNAUtilsException , NotationException , HELM2HandledException , ChemistryException , NucleotideLoadingException { checkRNA ( one ) ; checkRNA ( two ) ; List < ConnectionNotation > connections = new Array... | method to hybridize two PolymerNotations together if they are antiparallel |
141,592 | public static String getSequence ( PolymerNotation one ) throws RNAUtilsException , HELM2HandledException , ChemistryException { checkRNA ( one ) ; List < Nucleotide > nucleotideList = getNucleotideList ( one ) ; StringBuffer sb = new StringBuffer ( ) ; for ( int i = 0 ; i < nucleotideList . size ( ) ; i ++ ) { sb . ap... | method to get the rna sequence of the given PolymerNotation |
141,593 | public static String getModifiedNucleotideSequence ( PolymerNotation polymer ) throws RNAUtilsException , HELM2HandledException , ChemistryException { checkRNA ( polymer ) ; List < Nucleotide > nucleotides = getNucleotideList ( polymer ) ; StringBuilder sb = new StringBuilder ( ) ; for ( Nucleotide nucleotide : nucleot... | method to get the modifiedNucleotideSequence of the given PolymerNotation |
141,594 | public static String getNucleotideSequence ( PolymerNotation polymer ) throws NotationException , RNAUtilsException , HELM2HandledException , NucleotideLoadingException , ChemistryException { List < Nucleotide > nucleotides = getNucleotideList ( polymer ) ; StringBuffer sb = new StringBuffer ( ) ; int count = 0 ; Map <... | method to get the nucleotide sequence for the polymer |
141,595 | public static List < Nucleotide > getNucleotideList ( PolymerNotation polymer ) throws RNAUtilsException , HELM2HandledException , ChemistryException { checkRNA ( polymer ) ; List < Nucleotide > nucleotides = new ArrayList < Nucleotide > ( ) ; List < MonomerNotation > monomerNotations = polymer . getPolymerElements ( )... | method to get all nucleotides for one polymer |
141,596 | public static String getTrimmedNucleotideSequence ( PolymerNotation polymer ) throws RNAUtilsException , HELM2HandledException , ChemistryException { checkRNA ( polymer ) ; List < Nucleotide > list = getNucleotideList ( polymer ) ; int start = 0 ; Nucleotide na = list . get ( start ) ; while ( null == na . getBaseMonom... | method to get the trimmed nucleotide sequence |
141,597 | public static JKExceptionHandlerFactory getInstance ( ) { if ( JKExceptionHandlerFactory . instance == null ) { JKExceptionHandlerFactory . instance = new JKExceptionHandlerFactory ( ) ; } return JKExceptionHandlerFactory . instance ; } | Gets the single instance of ExceptionHandlerFactory . |
141,598 | public void setHandler ( final Class < ? extends Throwable > clas , final JKExceptionHandler handler ) { this . handlers . put ( clas , handler ) ; } | Sets the handler . |
141,599 | public void registerHanders ( String packageString ) { List < String > list = AnnotationDetector . scanAsList ( ExceptionHandler . class , packageString ) ; for ( String handler : list ) { JKExceptionHandler < ? extends Throwable > newInstance = JKObjectUtil . newInstance ( handler ) ; Class < ? extends Throwable > cla... | Register handers . |
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