code stringlengths 73 34.1k | label stringclasses 1
value |
|---|---|
public boolean unmodifiedWithoutPhosphate() {
if (getNotation() == null) {
return true;
} else {
// System.out.println("Contains [ " + getNotation().contains("[") +
// "\tContainsX " + getNotation().contains("["));
if (getNotation().contains("[") || getNotation().contains("X")) {
... | java |
public Monomer getBaseMonomer(MonomerStore monomerStore) {
String baseSymbol = getBaseSymbol();
if (baseSymbol != null && !baseSymbol.equalsIgnoreCase("")) {
try {
Map<String, Monomer> monomers = monomerStore.getMonomers(Monomer.NUCLIEC_ACID_POLYMER_TYPE);
Monomer m = monomers.get(baseSym... | java |
public Monomer getSugarMonomer(MonomerStore monomerStore) {
String sugarSymbol = getSugarSymbol();
if (sugarSymbol != null && !sugarSymbol.equalsIgnoreCase("")) {
try {
Map<String, Monomer> monomers = monomerStore.getMonomers(Monomer.NUCLIEC_ACID_POLYMER_TYPE);
Monomer m = monomers.get(sug... | java |
public String getLinkerNotation() {
String pSymbol = getPhosphateSymbol();
String result = null;
if (null == pSymbol || pSymbol.length() == 0) {
result = "";
} else {
if (pSymbol.length() > 1)
result = "[" + pSymbol + "]";
else
result = pSymbol;
}
return result;... | java |
public String getNucleosideNotation() {
int linkerLen = getLinkerNotation().length();
return notation.substring(0, notation.length() - linkerLen);
} | java |
public void addMonomer(Monomer monomer, boolean dbChanged)
throws IOException, MonomerException {
Map<String, Monomer> monomerMap = monomerDB.get(monomer.getPolymerType());
String polymerType = monomer.getPolymerType();
String alternateId = monomer.getAlternateId();
String smilesString = mono... | java |
public boolean hasMonomer(String polymerType, String alternateId) {
return ((monomerDB.get(polymerType) != null) && getMonomer(polymerType, alternateId) != null);
} | java |
public Monomer getMonomer(String polymerType, String alternateId) {
Map<String, Monomer> map1 = monomerDB.get(polymerType);
//alternateId = alternateId.toUpperCase();
return monomerDB.get(polymerType).get(alternateId);
} | java |
public synchronized void addNewMonomer(Monomer monomer) throws IOException,
MonomerException {
monomer.setNewMonomer(true);
addMonomer(monomer, true);
} | java |
public List<Monomer> getAllMonomersList() {
List<Monomer> monomers = new ArrayList<Monomer>();
for (String polymerType : getPolymerTypeSet()) {
Map<String, Monomer> map = getMonomers(polymerType);
monomers.addAll(map.values());
}
return monomers;
} | java |
public final static void addAnnotation(final AnnotationNotation notation, final int position,
final HELM2Notation helm2notation) {
helm2notation.getListOfAnnotations().add(position, notation);
} | java |
public final static void changeAnnotation(final AnnotationNotation notation, final int position,
final HELM2Notation helm2notation) {
helm2notation.getListOfAnnotations().set(position, notation);
} | java |
public final static void addConnection(final ConnectionNotation notation, final int position,
final HELM2Notation helm2notation) {
helm2notation.getListOfConnections().add(position, notation);
} | java |
public final static void changeConnection(final int position, final ConnectionNotation notation,
final HELM2Notation helm2notation) {
helm2notation.getListOfConnections().set(position, notation);
} | java |
public final static void addAnnotationToConnection(final int position, final String annotation,
final HELM2Notation helm2notation) {
helm2notation.getListOfConnections().get(position).setAnnotation(annotation);
} | java |
public final static void addGroup(final GroupingNotation notation, final int position,
final HELM2Notation helm2notation) {
helm2notation.getListOfGroupings().add(position, notation);
} | java |
public final static void changeGroup(final GroupingNotation notation, final int position,
final HELM2Notation helm2notation) {
helm2notation.getListOfGroupings().set(position, notation);
} | java |
public final static PolymerNotation addAnnotationToPolymer(final PolymerNotation polymer, final String annotation) {
if (polymer.getAnnotation() != null) {
return new PolymerNotation(polymer.getPolymerID(), polymer.getPolymerElements(),
polymer.getAnnotation() + " | " + annotation);
}
return new Poly... | java |
public final static PolymerNotation removeAnnotationOfPolmyer(PolymerNotation polymer) {
return new PolymerNotation(polymer.getPolymerID(), polymer.getPolymerElements(), null);
} | java |
public final static PolymerNotation addMonomerNotation(int position, PolymerNotation polymer,
MonomerNotation monomerNotation) {
polymer.getPolymerElements().getListOfElements().add(position, monomerNotation);
return polymer;
} | java |
public final static void changeMonomerNotation(int position, PolymerNotation polymer, MonomerNotation not) {
polymer.getPolymerElements().getListOfElements().set(position, not);
} | java |
public final static void deleteMonomerNotation(int position, PolymerNotation polymer) throws NotationException {
MonomerNotation monomerNotation = polymer.getPolymerElements().getListOfElements().get(position);
if (polymer.getPolymerElements().getListOfElements().size() == 1) {
throw new NotationException(mon... | java |
public final static void addAnnotationToMonomerNotation(PolymerNotation polymer, int position, String annotation) {
polymer.getPolymerElements().getListOfElements().get(position).setAnnotation(annotation);
} | java |
public final static void addCountToMonomerNotation(PolymerNotation polymer, int position, String count) {
polymer.getPolymerElements().getListOfElements().get(position).setCount(count);
} | java |
public final static void deleteAnnotationFromMonomerNotation(PolymerNotation polymer, int position) {
polymer.getPolymerElements().getListOfElements().get(position).setAnnotation(null);
} | java |
public final static void changePolymerNotation(int position, PolymerNotation polymer, HELM2Notation helm2notation) {
helm2notation.getListOfPolymers().set(position, polymer);
} | java |
public final static void addPolymerNotation(int position, PolymerNotation polymer, HELM2Notation helm2notation) {
helm2notation.getListOfPolymers().add(position, polymer);
} | java |
public final static void replaceMonomer(HELM2Notation helm2notation, String polymerType, String existingMonomerID,
String newMonomerID) throws NotationException, MonomerException,
ChemistryException, CTKException, IOException, JDOMException {
validateMonomerReplacement(polymerType, existingMonomerID, newMo... | java |
public final static MonomerNotation replaceMonomerNotation(MonomerNotation monomerNotation,
String existingMonomerID, String newMonomerID)
throws NotationException, ChemistryException, CTKException, MonomerLoadingException {
/* Nucleotide */
if (monomerNotation instanceof MonomerNotationUnitRNA) {
L... | java |
public final static MonomerNotationGroup replaceMonomerNotationGroup(MonomerNotationGroup monomerNotation,
String existingMonomerID, String newMonomerID) throws NotationException {
MonomerNotationGroup newObject = null;
boolean hasChanged = false;
StringBuilder sb = new StringBuilder();
String id = "";
... | java |
public final static MonomerNotationUnit produceMonomerNotationUnitWithOtherID(MonomerNotation monomerNotation,
String newID) throws NotationException {
MonomerNotationUnit result = new MonomerNotationUnit(newID, monomerNotation.getType());
if (monomerNotation.isAnnotationTrue()) {
result.setAnnotation(mon... | java |
public final static MonomerNotationList replaceMonomerNotationList(MonomerNotationList object,
String existingMonomerID, String newMonomerID)
throws NotationException, ChemistryException, CTKException, MonomerLoadingException {
MonomerNotationList newObject = null;
boolean hasChanged = false;
StringB... | java |
private final static String generateIDMonomerNotation(String id, String count, String annotation) {
if (id.length() > 1) {
id = "[" + id + "]";
}
String result = id;
try {
if (!(Integer.parseInt(count) == 1)) {
result += "'" + count + "'";
}
} catch (NumberFormatException e) {
result... | java |
private final static String generateIDRNA(String id, String count, String annotation)
throws MonomerLoadingException, ChemistryException, CTKException {
String result = id;
if (result.startsWith("[") && result.endsWith("]")) {
result = id.substring(1, id.length() - 1);
}
if (MonomerFactory.getInstan... | java |
private final static List<String> generateIDForNucleotide(MonomerNotationUnitRNA object, String existingMonomerID,
String newMonomerID) throws MonomerLoadingException, ChemistryException, CTKException {
List<String> result = new ArrayList<String>();
String hasChanged = null;
StringBuilder sb = new StringBu... | java |
private static String generateGroupElement(String id, List<Double> list) {
StringBuilder sb = new StringBuilder();
if (list.size() == 1) {
if (list.get(0) == -1.0) {
sb.append(id + ":");
sb.append("?" + "-");
} else if (list.get(0) == 1.0) {
sb.append(id + ":");
} else {
sb.appen... | java |
public static final void replaceSMILESWithTemporaryIds(HELM2Notation helm2notation) throws NotationException,
HELM2HandledException, ChemistryException, CTKException, MonomerLoadingException, JDOMException {
for (int i = 0; i < helm2notation.getListOfPolymers().size(); i++) {
/* First save intern smiles to t... | java |
public static void hybridize(HELM2Notation helm2notation) throws NotationException, RNAUtilsException,
HELM2HandledException, org.helm.notation2.exception.NotationException, ChemistryException {
if (HELM2NotationUtils.getAllBasePairConnections(helm2notation.getListOfConnections()).isEmpty()
&& HELM2Notation... | java |
public void setApplicationMap(final Map<String, Object> applicationMap) {
JKThreadLocal.setValue(JKContextConstants.APPLICATION_MAP, applicationMap);
} | java |
public void setRequestMap(final Map<String, Object> requestMap) {
JKThreadLocal.setValue(JKContextConstants.HTTP_REQUEST_MAP, requestMap);
} | java |
public void setSessionMap(final Map<String, Object> sessionMap) {
JKThreadLocal.setValue(JKContextConstants.HTTP_SESSION_MAP, sessionMap);
} | java |
private static String compress(String str) throws EncoderException {
ByteArrayOutputStream rstBao = null;
GZIPOutputStream zos = null;
try {
rstBao = new ByteArrayOutputStream();
zos = new GZIPOutputStream(rstBao);
zos.write(str.getBytes());
IOUtils.closeQuietly(zos);
byte[] bytes =... | java |
private static String decompress(String str) throws EncoderException {
/* First base64 decode the string */
byte[] bytes = Base64.decodeBase64(str);
GZIPInputStream zi = null;
try {
zi = new GZIPInputStream(new ByteArrayInputStream(bytes));
InputStreamReader reader = new InputStreamReader(zi... | java |
public MemoryFileAttributes addDir( EightyPath dir, Principals principals ) {
if( content.get( dir ).isPresent() ) {
throw new IllegalArgumentException( "path exists already" );
}
if( !dir.isAbsolute() || dir.getParent() == null ) {
throw new IllegalArgumentException( "... | java |
public static Map<String, Attachment> loadAttachments(InputStream in) throws IOException {
ObjectMapper mapper = new ObjectMapper();
TypeReference<TreeMap<String, Attachment>> typeRef = new TypeReference<TreeMap<String, Attachment>>() {
};
TreeMap<String, Attachment> attachments;
try {
attachments ... | java |
public static boolean validateAttachment(Attachment currentAttachment) {
try {
currentAttachment.getId();
if (currentAttachment.getAlternateId() == "null" || currentAttachment.getAlternateId().isEmpty()) {
return false;
}
if (currentAttachment.getCapGroupName() == "null" || currentAttachment.g... | java |
public static void checkAllowedPrivilige(final JKPrivilige privilige) {
logger.debug("checkAllowedPrivilige() : ", privilige);
final JKAuthorizer auth = getAuthorizer();
auth.checkAllowed(privilige);
} | java |
public static boolean matchPassword(String plain, JKUser user) {
JK.implementMe();
return JKSecurityUtil.encode(plain).equals(user.getPassword());
} | java |
public static JKPrivilige createPrivilige(String name, JKPrivilige parent, int number) {
logger.trace("createPriviligeObject(): Id : ", ".name", name, ", Parent:[", parent, "] , ", number);
JKPrivilige p = new JKPrivilige(name, parent, number);
p.setDesc(p.getFullName());
return p;
} | java |
public static HELM2Notation readPeptide(String notation)
throws FastaFormatException, NotationException, ChemistryException {
HELM2Notation helm2notation = new HELM2Notation();
PolymerNotation polymer = new PolymerNotation("PEPTIDE1");
helm2notation.addPolymer(new PolymerNotation(polymer.getPolymerID(),
... | java |
public static String getPeptideSequenceFromNotation(HELM2Notation helm2notation) throws HELM2HandledException,
PeptideUtilsException, org.helm.notation2.exception.NotationException, ChemistryException {
List<PolymerNotation> polymers = helm2notation.getListOfPolymers();
StringBuffer sb = new StringBuffer();
... | java |
public static String getNucleotideNaturalAnalogSequenceFromNotation(HELM2Notation helm2Notation)
throws NotationException, HELM2HandledException, ChemistryException {
List<PolymerNotation> polymers = helm2Notation.getListOfPolymers();
StringBuffer sb = new StringBuffer();
for (PolymerNotation polymer : pol... | java |
public static String getPeptideNaturalAnalogSequenceFromNotation(HELM2Notation helm2Notation)
throws HELM2HandledException, PeptideUtilsException, NotationException, ChemistryException {
List<PolymerNotation> polymers = helm2Notation.getListOfPolymers();
StringBuffer sb = new StringBuffer();
for (PolymerNo... | java |
public static void setDefaultExecutor(Executor executor) {
Class<?> c = null;
Field field = null;
try {
c = Class.forName("android.os.AsyncTask");
field = c.getDeclaredField("sDefaultExecutor");
field.setAccessible(true);
field.set(null, executor);... | java |
public static Executor getDefaultExecutor() {
Executor exec = null;
Class<?> c = null;
Field field = null;
try {
c = Class.forName("android.os.AsyncTask");
field = c.getDeclaredField("sDefaultExecutor");
field.setAccessible(true);
exec = (... | java |
public static Nucleotide convertToNucleotide(String id, boolean last) throws MonomerException, org.helm.notation2.exception.NotationException, ChemistryException, NucleotideLoadingException,
NotationException {
Map<String, String> reverseNucMap = NucleotideFactory.getInstance().getReverseNucleotideTemplateM... | java |
public static boolean validateSimpleNotationForRNA(String polymerNotation) throws org.helm.notation2.parser.exceptionparser.NotationException {
getMonomerIDListFromNucleotide(polymerNotation);
return true;
} | java |
@Override
public void dragged(IEventMotion e) {
if(paletteDiagram.getSelectedCommand() == ECommands.SELECT.toString()) {
if(!itWasDragging) {
itWasDragging = asmDiagramUml.tryToDragging(e.getX(), e.getY());
}
else {
asmDiagramUml.tryToDragging(e.getX(), e.getY());
}
}
... | java |
public static HELM2Notation generatePeptidePolymersFromFASTAFormatHELM1(String fasta)
throws FastaFormatException, ChemistryException {
helm2notation = new HELM2Notation();
if (null == fasta) {
LOG.error("Peptide Sequence must be specified");
throw new FastaFormatException("Peptide Sequence must be sp... | java |
private static void initMapNucleotides() throws FastaFormatException {
try {
nucleotides = NucleotideFactory.getInstance().getNucleotideTemplates().get("HELM Notation");
} catch (IOException e) {
e.printStackTrace();
LOG.error("NucleotideFactory can not be initialized");
throw new FastaFormatExcep... | java |
private static void initMapTransformNucleotides() {
transformNucleotides = new HashMap<String, String>();
for (Map.Entry e : nucleotides.entrySet()) {
transformNucleotides.put(e.getValue().toString(), e.getKey().toString());
}
} | java |
private static void initMapNucleotidesNaturalAnalog() throws FastaFormatException, ChemistryException {
try {
nucleotidesNaturalAnalog = MonomerFactory.getInstance().getMonomerDB().get("RNA");
} catch (IOException e) {
e.printStackTrace();
LOG.error("Nucleotides can not be initialized");
throw new... | java |
private static void initMapAminoAcid() throws FastaFormatException, ChemistryException {
try {
aminoacids = MonomerFactory.getInstance().getMonomerDB().get("PEPTIDE");
} catch (IOException e) {
e.printStackTrace();
LOG.error("AminoAcids can not be initialized");
throw new FastaFormatException(e.ge... | java |
protected static String generateFastaFromPeptide(List<Monomer> monomers) {
StringBuilder fasta = new StringBuilder();
for (Monomer monomer : monomers) {
fasta.append(monomer.getNaturalAnalog());
}
return fasta.toString();
} | java |
public static String generateFastaFromRNAPolymer(List<PolymerNotation> polymers)
throws FastaFormatException, ChemistryException {
StringBuilder fasta = new StringBuilder();
for (PolymerNotation polymer : polymers) {
String header = polymer.getPolymerID().getId();
if (polymer.getAnnotation() != null) ... | java |
protected static String generateFastaFromRNA(List<Monomer> monomers) {
StringBuilder fasta = new StringBuilder();
for (Monomer monomer : monomers) {
if (monomer.getMonomerType().equals(Monomer.BRANCH_MOMONER_TYPE)) {
fasta.append(monomer.getNaturalAnalog());
}
}
return fasta.toString();
} | java |
public static String generateFasta(HELM2Notation helm2Notation2) throws FastaFormatException, ChemistryException {
List<PolymerNotation> polymersPeptides = new ArrayList<PolymerNotation>();
List<PolymerNotation> polymerNucleotides = new ArrayList<PolymerNotation>();
StringBuilder fasta = new StringBuilder();
... | java |
public static HELM2Notation convertIntoAnalogSequence(HELM2Notation helm2Notation)
throws FastaFormatException, AnalogSequenceException, ChemistryException, CTKException {
initMapAminoAcid();
initMapNucleotides();
initMapNucleotidesNaturalAnalog();
initMapTransformNucleotides();
/*
* transform/co... | java |
private static PolymerNotation convertPeptideIntoAnalogSequence(PolymerNotation polymer)
throws AnalogSequenceException {
for (int i = 0; i < polymer.getPolymerElements().getListOfElements().size(); i++) {
/* Change current MonomerNotation */
polymer.getPolymerElements().getListOfElements().set(i,
... | java |
private static MonomerNotation generateMonomerNotationRNA(MonomerNotation current) throws AnalogSequenceException {
MonomerNotation change = null;
try {
/* simple MonomerNotationUnit */
if (current instanceof MonomerNotationUnit) {
change = new MonomerNotationUnit(changeIdForRNA(current), current.g... | java |
private static PolymerNotation convertRNAIntoAnalogSequence(PolymerNotation polymer)
throws AnalogSequenceException {
/* change only if it is possible */
for (int i = 0; i < polymer.getPolymerElements().getListOfElements().size(); i++) {
polymer.getPolymerElements().getListOfElements().set(i,
gene... | java |
private static String changeIdForRNA(MonomerNotation monomerNotation) {
if (monomerNotation instanceof MonomerNotationUnitRNA) {
StringBuilder changeid = new StringBuilder();
for (MonomerNotation not : ((MonomerNotationUnitRNA) monomerNotation).getContents()) {
Monomer monomer = nucleotidesNaturalAnal... | java |
private boolean checkHostPart(final String label, final Problems problems, final String compName) {
boolean result = true;
if (label.length() > 63) {
problems.add(ValidationBundle.getMessage(HostNameValidator.class, "LABEL_TOO_LONG", label)); // NOI18N
result = false;
}
if (label.length() == 0) {
probl... | java |
public static String getMacAddress() {
try {
List<String> macAddress = new ArrayList<String>();
Enumeration<NetworkInterface> enumNetWorkInterface = NetworkInterface.getNetworkInterfaces();
while (enumNetWorkInterface.hasMoreElements()) {
NetworkInterface netWorkInterface = enumNetWorkInterface.nextElem... | java |
public static Properties getSystemInfo() {
logger.debug("getSystemInfo()");
if (MachineInfo.systemInfo == null) {
if (!JKIOUtil.isWindows()) {
throw new IllegalStateException("this feature is only supported on windows");
}
final byte[] sourceFileContents = JKIOUtil.readFileAsByteArray("/native/jk.dll")... | java |
public static Class<?> getExceptionCallerClass(final Throwable t) {
final StackTraceElement[] stackTrace = t.getStackTrace();
for (final StackTraceElement stackTraceElement : stackTrace) {
logger.debug(stackTraceElement.getClassName().concat(".").concat(stackTraceElement.getMethodName()));
}
return null... | java |
public static String getMainClassName() {
StackTraceElement trace[] = Thread.currentThread().getStackTrace();
if (trace.length > 0) {
return trace[trace.length - 1].getClassName();
}
return "Unknown";
} | java |
public static HELM2Notation getSiRNANotation(String senseSeq, String antiSenseSeq)
throws NotationException, FastaFormatException, HELM2HandledException, RNAUtilsException,
org.helm.notation2.exception.NotationException, ChemistryException, CTKException,
NucleotideLoadingException {
return getSirnaNotati... | java |
public static HELM2Notation getSirnaNotation(String senseSeq, String antiSenseSeq, String rnaDesignType)
throws NotationException, FastaFormatException, HELM2HandledException, RNAUtilsException,
org.helm.notation2.exception.NotationException, ChemistryException, CTKException,
NucleotideLoadingException {
... | java |
private static List<ConnectionNotation> hybridization(PolymerNotation one, PolymerNotation two,
String rnaDesignType) throws NotationException, HELM2HandledException, RNAUtilsException,
org.helm.notation2.exception.NotationException, ChemistryException, NucleotideLoadingException {
List<ConnectionNotation>... | java |
private static List<ConnectionNotation> hybridizationWithLengthFromStart(PolymerNotation one, PolymerNotation two,
String senseAnalogSeq, String antisenseAnalogSeq, int lengthFromStart) throws NotationException {
List<ConnectionNotation> connections = new ArrayList<ConnectionNotation>();
ConnectionNotation co... | java |
private static boolean validateSiRNADesign(PolymerNotation one, PolymerNotation two, String rnaDesignType)
throws RNAUtilsException, HELM2HandledException, NotationException, ChemistryException {
if (NucleotideParser.RNA_DESIGN_NONE.equalsIgnoreCase(rnaDesignType)) {
return true;
}
if (!NucleotidePar... | java |
public synchronized Map<String, Map<String, Monomer>> getMonomerDB(boolean includeNewMonomers) {
if (includeNewMonomers) {
return monomerDB;
} else {
Map<String, Map<String, Monomer>> reducedMonomerDB = new TreeMap<String, Map<String, Monomer>>(
String.CASE_INSENSITIVE_ORDER);
for (String polymerType ... | java |
public static MonomerFactory getInstance() throws MonomerLoadingException, ChemistryException {
if (null == instance) {
refreshMonomerCache();
}
else if (MonomerStoreConfiguration.getInstance().isUseWebservice()
&& MonomerStoreConfiguration.getInstance().isUpdateAutomatic()) {
refreshMonomerCache();
... | java |
public synchronized void addNewMonomer(Monomer monomer) throws IOException, MonomerException {
monomer.setNewMonomer(true);
addMonomer(monomerDB, smilesMonomerDB, monomer);
dbChanged = true;
} | java |
public MonomerCache buildMonomerCacheFromXML(String monomerDBXML)
throws MonomerException, IOException, JDOMException, ChemistryException, CTKException {
ByteArrayInputStream bais = new ByteArrayInputStream(monomerDBXML.getBytes());
return buildMonomerCacheFromXML(bais);
} | java |
public synchronized void merge(MonomerCache remoteMonomerCache) throws IOException, MonomerException {
Map<Monomer, Monomer> conflicts = getConflictedMonomerMap(remoteMonomerCache);
if (conflicts.size() > 0) {
throw new MonomerException("Local new monomer and remote monomer database conflict found");
} else {
... | java |
public synchronized void setMonomerCache(MonomerCache remoteMonomerCache) throws IOException, MonomerException {
monomerDB = remoteMonomerCache.getMonomerDB();
attachmentDB = remoteMonomerCache.getAttachmentDB();
smilesMonomerDB = remoteMonomerCache.getSmilesMonomerDB();
dbChanged = true;
} | java |
private static Map<String, Attachment> buildAttachmentDB() throws IOException {
Map<String, Attachment> map = new TreeMap<String, Attachment>(String.CASE_INSENSITIVE_ORDER);
if (MonomerStoreConfiguration.getInstance().isUseExternalAttachments()) {
map = AttachmentLoader.loadAttachments(
new FileInputStre... | java |
public void saveMonomerCache() throws IOException, MonomerException {
File f = new File(NOTATION_DIRECTORY);
if (!f.exists()) {
f.mkdir();
}
MonomerCache cache = new MonomerCache();
cache.setMonomerDB(getMonomerDB(false));
cache.setAttachmentDB(getAttachmentDB());
cache.setSmilesMonomerDB(getSmilesMono... | java |
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.... | java |
public static List<String> scanAsList(final Class<? extends Annotation> clas, final String... basePackage) {
final List<String> classes = new ArrayList<>();
scan(clas, basePackage, new AnnotationHandler() {
@Override
public void handleAnnotationFound(String className) {
classes.add(className);
}
});... | java |
@Override
public void refreshGuiAndShowFile(File file) {
if(rootNode.getChildCount() > 0) {
rootNode.removeAllChildren();
treeModel.reload();
}
if(guiMain.getAsmProjectUml().getProjectUml() != null) {
addTreeNodes(file);
guiMain.getMenuMain().setVisibleProjectMenu(true);
}
... | java |
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<?>) ... | java |
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;
} | java |
public static void validateNull(String name, Object object) {
if (object == null) {
throw new IllegalStateException(name.concat(" cannot be null"));
}
} | java |
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);
}
} | java |
public static char[] readPassword(String msg) {
Console console = System.console();
if (console != null) {
return console.readPassword();
}
// console not available, most likely because of running inside IDE, try normal
scanner = getScanner();
System.out.print(msg);
return scanner.nextLine().to... | java |
public static void printOnce(Object msg) {
if (messagesCache.get(msg.hashCode()) == null) {
JK.printBlock(msg);
messagesCache.put(msg.hashCode(), msg);
}
} | java |
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;
} | java |
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