code stringlengths 73 34.1k | label stringclasses 1
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public String generateNaturalAnalogSequenceRNA(String notation)
throws org.helm.notation2.parser.exceptionparser.NotationException, HELM2HandledException,
ValidationException, MonomerLoadingException, ChemistryException {
String result = SequenceConverter.getNucleotideNaturalAnalogSequenceFromNotation(valida... | java |
public String convertMolFileSMILESWithAtomMapping(String molfile, List<Attachment> attachments) throws CTKException, ChemistryException{
return SMILES.convertMolToSMILESWithAtomMapping(molfile, attachments);
} | java |
public static List<MonomerNotation> getListOfMonomerNotation(List<PolymerNotation> polymers) {
List<MonomerNotation> items = new ArrayList<MonomerNotation>();
for (PolymerNotation polymer : polymers) {
items.addAll(polymer.getListMonomers());
}
return items;
} | java |
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 < monomerNotations.size();... | java |
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(... | java |
public static JKLocale valueOf(final String localeString) {
return localeString.equals(ARABIC.shortName) ? ARABIC : ENGLISH;
} | java |
public String getAuditText() {
final StringBuffer b = new StringBuffer();
b.append(getOldValue().replaceAll(",", "\n"));
b.append("-----------------------------------------\n");
b.append(getNewValue().replaceAll(",", "\n"));
b.append("-----------------------------------------\n");
return b.toString();
} | java |
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... | java |
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... | java |
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... | java |
public static boolean isAuthenticed(String host, int port, String userName, String password) throws NamingException {
log.info("isAuthenticed");
// Set up the environment for creating the initial context
Hashtable<String, String> env = new Hashtable<String, String>();
env.put(Context.INITIAL_CONTEXT_FACTORY, "c... | java |
protected static String fixKey(final String key) {
if (key.startsWith(getKeyPrefix())) {
return key;
}
return getKeyPrefix() + "-" + key;
} | java |
public static float getFloat(final String key, final float def) {
try {
return systemRoot.getFloat(fixKey(key), def);
} catch (final Exception e) {
// just eat the exception to avoid any system
// crash on system issues
return def;
}
} | java |
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.split(";");
for (final St... | java |
public static int getInt(final String key, final int def) {
try {
return systemRoot.getInt(fixKey(key), def);
} catch (final Exception e) {
// just eat the exception to avoid any system crash on system issues
return def;
}
} | java |
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("")) {
// end the previous record
buf.append(";");
}
final String key... | java |
public static void setKeyPrefix(final String keyPrefix) {
UserPreferences.keyPrefix = keyPrefix;
try {
systemRoot.sync();
} catch (final Exception e) {
JKExceptionUtil.handle(e);
}
} | java |
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(local... | java |
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_NUC... | java |
@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;
} | java |
private void readConfigFile() {
File configFile = new File(CONFIG_FILE_PATH);
/* config file is not there -> create config file with default */
if (!configFile.exists()) {
resetConfigToDefault();
}
try {
PropertiesConfiguration conf = new PropertiesConfiguration(CONFIG_FILE_PATH... | java |
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 ;
i... | java |
@Override
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, idComm... | java |
public static String getHELMNotationString(Element rootElement) {
Element helmNotationElement = rootElement.getChild("HelmNotation");
return helmNotationElement.getText();
} | java |
public static String getComplexNotationString(Element rootElement) {
Element helmNotationElement = rootElement.getChild("HelmNotation");
return helmNotationElement.getText();
} | java |
public static MonomerStore getMonomerStore(Element rootElement)
throws MonomerException, IOException {
MonomerStore monomerStore = new MonomerStore();
Element monomerListElement = rootElement.getChild("Monomers");
if (monomerListElement != null) {
@SuppressWarnings("unchecked")
List<... | java |
public boolean isNumeric() {
final Class c = getColumnClass();
return c.equals(Integer.class) || c.equals(Float.class) || c.equals(Long.class) || c.equals(BigDecimal.class);
} | java |
public void setColumnClassName(final String columnClassName) throws ClassNotFoundException {
if (columnClassName.equals("byte[]")) {
setColumnClass(Object.class);
} else {
setColumnClass(Class.forName(columnClassName));
}
this.columnClassName = columnClassName;
} | java |
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("Convert smi... | java |
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);
final ObjectInputStre... | java |
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;
} | java |
private static Vector newVector(final int size) {
final Vector v = new Vector(size);
v.setSize(size);
return v;
} | java |
@Override
public String getColumnName(final int column) {
Object id = null;
// This test is to cover the case when
// getColumnCount has been subclassed by mistake ...
if (column < this.columnIdentifiers.size() && column >= 0) {
id = this.columnIdentifiers.elementAt(column);
}
return id == null ... | java |
private void justifyRows(final int from, final int to) {
// Sometimes the DefaultTableModel is subclassed
// instead of the AbstractTableModel by mistake.
// Set the number of rows for the case when getRowCount
// is overridden.
this.dataVector.setSize(getRowCount());
for (int i = from; i < to; i++)... | java |
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.toExter... | java |
public static byte[] readStream(final InputStream inStream) {
try {
return IOUtils.toByteArray(inStream);
} catch (IOException e) {
throw new JKException(e);
}
//
// try {
// DataInputStream in = null;
// try {
// in = new DataInputStream(inStream);
// int ch;
//
// List<Byte> b... | java |
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,... | java |
public static Reader getReader(String name) {
InputStream inputStream = getInputStream(name);
if (inputStream != null) {
BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
return reader;
}
return null;
} | java |
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);
} | java |
public static String removeExtension(String fileName) {
final String separator = FILE_SEPARATOR;
String filename;
// Remove the path upto the filename.
final int lastSeparatorIndex = fileName.lastIndexOf(separator);
if (lastSeparatorIndex == -1) {
filename = fileName;
} else {
filename = fileN... | java |
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;
}
} | java |
public static Properties readPropertiesStream(InputStream inputStream) {
try {
final Properties prop = new Properties();
// try to read in utf 8
prop.load(new InputStreamReader(inputStream, Charset.forName("utf-8")));
JKCollectionUtil.fixPropertiesKeys(prop);
return prop;
} catch (IOException ... | java |
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.handle... | java |
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;
}
} | java |
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);
}
} | java |
public static String getSqlFile(String fileName) {
String file = "/jk/sql/".concat(fileName);
logger.debug("Loading sql file: ", file);
return readFile(file);
} | java |
public static void clearTempFiles() {
String userFolderPath = getUserFolderPath(false);
File file = new File(userFolderPath);
deleteDir(file);
} | java |
public static void startFakeThread(ServerSocket server) {
Thread thread = new Thread(new FakeRunnable(server));
thread.start();
} | java |
public static String getReportsOutPath(boolean appendFileSeprator) {
String userLocalPath = getUserFolderPath(true);
String reportPath = userLocalPath + REPORTS_OUT_PATH;
checkFolderPath(reportPath, true);// to create the folder if not exist
if (appendFileSeprator) {
reportPath += FILE_SEPARATOR;
}
... | java |
public static List<String> getFilesInFolder(String folder, String ext) {
// tryto find using normal file system lookup
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.endsW... | java |
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());
FileUti... | java |
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.toURI());
... | java |
public static JKConfig readConfigFile(String configFileName) {
URL url = getURL(configFileName);
logger.debug(configFileName + " Url is ", url.toString());
JKConfig config = new JKConfig(url);
return config;
} | java |
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) {... | java |
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;
} | java |
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();
} | java |
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;
} | java |
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.setSSLOnConnect(isSecured());
if(this.bcc!... | java |
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;
} | java |
public static float toFloat(final Object value) {
if (value instanceof Float) {
return (float) value;
}
if (value == null) {
return 0;
}
return new Float(value.toString());
} | java |
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.getTime());
... | java |
public static boolean toBoolean(Object value, boolean defaultValue) {
boolean result;// = defaultValue;
if (value != null) {
if (value instanceof Boolean) {
return ((Boolean) value).booleanValue();
}
if (value.toString().trim().equals("1") || value.toString().trim().toLowerCase().equals("true")... | java |
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();
... | java |
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);
} | java |
public static void validateNotationObjects(HELM2Notation helm2notation) throws PolymerIDsException,
MonomerException, GroupingNotationException, ConnectionNotationException, NotationException,
ChemistryException, MonomerLoadingException, org.helm.notation2.parser.exceptionparser.NotationException {
LOG.info(... | java |
protected static boolean validateMonomers(List<MonomerNotation> mon) throws ChemistryException,
MonomerLoadingException, org.helm.notation2.parser.exceptionparser.NotationException {
for (MonomerNotation monomerNotation : mon) {
if (!(isMonomerValid(monomerNotation.getUnit(), monomerNotation.getType()))) {
... | java |
private static boolean isConnectionSpecific(ConnectionNotation connectionNotation) {
String connection = connectionNotation.getSourceUnit() + ":" + connectionNotation.getrGroupSource() + "-"
+ connectionNotation.getTargetUnit() + ":" + connectionNotation.getrGroupTarget();
/* check for specific interaction *... | java |
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>();
/* The monomer's position in the poly... | java |
public static boolean validateGrouping(HELM2Notation helm2notation) {
List<GroupingNotation> listGroupings = helm2notation.getListOfGroupings();
List<String> listPolymerIDs = helm2notation.getPolymerAndGroupingIDs();
/* validate each group */
for (GroupingNotation grouping : listGroupings) {
/* check ... | java |
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 (listPolymerI... | java |
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");
}
} | java |
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.getInstance();
/*... | java |
private static void checkPolymerIDSConnection(ConnectionNotation not, List<String> listPolymerIDs)
throws PolymerIDsException {
/* the polymer ids have to be there */
checkExistenceOfPolymerID(not.getSourceId().getId(), listPolymerIDs);
checkExistenceOfPolymerID(not.getTargetId().getId(), listPolymerIDs);
... | java |
public static List<Monomer> getAllMonomers(MonomerNotation not, int position) throws HELM2HandledException,
MonomerException, NotationException, ChemistryException, CTKException, MonomerLoadingException {
List<Monomer> monomers = new ArrayList<Monomer>();
MonomerFactory monomerFactory = MonomerFactory.getIn... | java |
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>();
MonomerFactory monome... | java |
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 is not there");
throw new Attac... | java |
private static boolean checkSingleAttachment(List<Monomer> monomers, String rGroup, HELM2Notation helm2notation,
ConnectionNotation not, InterConnections interconnection, String id) throws AttachmentException {
for (Monomer monomer : monomers) {
/* Are the attachment points there */
checkAttachmentPoin... | java |
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.getContents().get(... | java |
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("[", "");
id... | java |
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");
} | java |
public static boolean areAntiparallel(PolymerNotation polymerOne, PolymerNotation polymerTwo)
throws RNAUtilsException, HELM2HandledException, ChemistryException, NucleotideLoadingException {
checkRNA(polymerOne);
checkRNA(polymerTwo);
PolymerNotation antiparallel = getAntiparallel(polymerOne);
String s... | java |
public static String getMaxMatchFragment(String seq1, String seq2) throws NotationException {
return getMaxMatchFragment(seq1, seq2, MINUMUM_MATCH_FRAGMENT_LENGTH);
} | java |
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())) {
throw new Not... | java |
public static void removeLastP(PolymerNotation polymer)
throws RNAUtilsException, NotationException, HELM2HandledException {
checkRNA(polymer);
/* Get last monomerNotation */
MonomerNotation lastObject = polymer.getPolymerElements().getListOfElements()
.get(polymer.getPolymerElements().getListOfElemen... | java |
public static void addLastP(PolymerNotation polymer)
throws RNAUtilsException, NotationException, HELM2HandledException {
checkRNA(polymer);
/* Get last monomerNotation */
MonomerNotation lastObject = polymer.getPolymerElements().getListOfElements()
.get(polymer.getPolymerElements().getListOfElements... | java |
public static PolymerNotation getInverse(PolymerNotation polymer) throws RNAUtilsException, org.helm.notation2.exception.NotationException, ChemistryException, NucleotideLoadingException {
checkRNA(polymer);
PolymerNotation inverse;
try {
inverse = SequenceConverter.readRNA(generateInverse(polymer).toStrin... | java |
public static PolymerNotation getReverseComplement(PolymerNotation polymer) throws RNAUtilsException, org.helm.notation2.exception.NotationException, ChemistryException, NucleotideLoadingException {
checkRNA(polymer);
PolymerNotation complementReversePolymer;
try {
complementReversePolymer = SequenceConver... | java |
private static StringBuilder generateInverse(PolymerNotation polymer) throws HELM2HandledException,
RNAUtilsException, org.helm.notation2.exception.NotationException, ChemistryException {
initComplementMap();
String sequence = getNaturalAnalogSequence(polymer);
StringBuilder sb = new StringBuilder(sequence... | java |
public static boolean hasNucleotideModification(PolymerNotation polymer) throws NotationException {
for (MonomerNotation current : polymer.getPolymerElements().getListOfElements()) {
if (hasModification(current)) {
return true;
}
}
return false;
} | java |
private static boolean hasModification(MonomerNotation monomerNotation) throws NotationException {
if (monomerNotation instanceof MonomerNotationUnitRNA) {
if (hasModification((MonomerNotationUnitRNA) monomerNotation)) {
return true;
}
} else if (monomerNotation instanceof MonomerNotationGroup) {
... | java |
private static boolean hasModification(MonomerNotationUnitRNA monomerNotation) {
if (monomerNotation.getUnit().contains("[") || monomerNotation.getUnit().contains("(X)")
|| monomerNotation.getUnit().endsWith(")")) {
return true;
}
return false;
} | java |
public static List<ConnectionNotation> hybridizeAntiparallel(PolymerNotation one, PolymerNotation two)
throws RNAUtilsException, NotationException, HELM2HandledException,
ChemistryException, NucleotideLoadingException {
checkRNA(one);
checkRNA(two);
List<ConnectionNotation> connections = new ArrayLis... | java |
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.append(nuc... | java |
public static String getModifiedNucleotideSequence(PolymerNotation polymer)
throws RNAUtilsException, HELM2HandledException, ChemistryException {
checkRNA(polymer);
List<Nucleotide> nucleotides = getNucleotideList(polymer);
StringBuilder sb = new StringBuilder();
for (Nucleotide nucleotide : nucleotides... | java |
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<S... | java |
public static List<Nucleotide> getNucleotideList(PolymerNotation polymer)
throws RNAUtilsException, HELM2HandledException, ChemistryException {
checkRNA(polymer);
List<Nucleotide> nucleotides = new ArrayList<Nucleotide>();
/* check for HELM2Elements */
List<MonomerNotation> monomerNotations = polymer.ge... | java |
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.getBaseMonomer())... | java |
public static JKExceptionHandlerFactory getInstance() {
if (JKExceptionHandlerFactory.instance == null) {
JKExceptionHandlerFactory.instance = new JKExceptionHandlerFactory();
}
return JKExceptionHandlerFactory.instance;
} | java |
public void setHandler(final Class<? extends Throwable> clas, final JKExceptionHandler handler) {
this.handlers.put(clas, handler);
} | java |
public void registerHanders(String packageString) {
List<String> list = AnnotationDetector.scanAsList(ExceptionHandler.class, packageString);
for (String handler : list) {
// System.out.println(handler);
JKExceptionHandler<? extends Throwable> newInstance = JKObjectUtil.newInstance(handler);
Class<? e... | java |
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