id stringlengths 25 27 | content stringlengths 190 15.4k | max_stars_repo_path stringlengths 31 217 |
|---|---|---|
robustness-copilot_data_701 | /**
* Writes the fields of the given node into the generator.
*/
private void writeFieldsOfNode(JsonGenerator generator, JsonNode node) throws IOException{
if (node != null) {
for (Iterator<Entry<String, JsonNode>> fields = node.fields(); fields.hasNext(); ) {
Entry<String, JsonNode> field = fields.next();
generator.writeFieldName(field.getKey());
generator.writeTree(field.getValue());
}
}
} | /src/main/java/net/logstash/logback/composite/GlobalCustomFieldsJsonProvider.java |
robustness-copilot_data_702 | /**
* Method to deal with distance calculation when only the x and y-components
* of the coordinates are used. The elevation (z component) is ignored,
* whether it is available or not.
* (xy-plane)
* @param coord
* @param other
* @return
*/
public static double calcProjectedEuclideanDistance(Coord coord, Coord other){
double xDiff = other.getX() - coord.getX();
double yDiff = other.getY() - coord.getY();
return Math.sqrt((xDiff * xDiff) + (yDiff * yDiff));
} | /matsim/src/main/java/org/matsim/core/utils/geometry/CoordUtils.java |
robustness-copilot_data_703 | /**
* Create the port alias and attach it to the process.
*
* @param userId the name of the calling user
* @param portAlias the port alias values
* @param processGUID the unique identifier of the process
* @param externalSourceName the unique name of the external source
*
* @return unique identifier of the port alias in the repository
*
* @throws InvalidParameterException the bean properties are invalid
* @throws UserNotAuthorizedException user not authorized to issue this request
* @throws PropertyServerException problem accessing the property server
*/
public String createPortAlias(String userId, PortAlias portAlias, String processGUID, String externalSourceName) throws InvalidParameterException, UserNotAuthorizedException, PropertyServerException{
return createPort(userId, portAlias, PORT_ALIAS_TYPE_NAME, processGUID, externalSourceName);
} | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEnginePortHandler.java |
robustness-copilot_data_704 | /**
* Private method that actually parses the input to read a ChemFile
* object.
*
* Each PMP frame is stored as a Crystal in a ChemModel. The PMP
* file is stored as a ChemSequence of ChemModels.
*
* @return A ChemFile containing the data parsed from input.
*/
private IChemFile readChemFile(IChemFile chemFile){
IChemSequence chemSequence;
IChemModel chemModel;
ICrystal crystal;
try {
String line = readLine();
while (input.ready() && line != null) {
if (line.startsWith("%%Header Start")) {
while (input.ready() && line != null && !(line.startsWith("%%Header End"))) {
if (line.startsWith("%%Version Number")) {
String version = readLine().trim();
if (!version.equals("3.00")) {
logger.error("The PMPReader only supports PMP files with version 3.00");
return null;
}
}
line = readLine();
}
} else if (line.startsWith("%%Model Start")) {
modelStructure = chemFile.getBuilder().newInstance(IAtomContainer.class);
while (input.ready() && line != null && !(line.startsWith("%%Model End"))) {
Matcher objHeaderMatcher = objHeader.matcher(line);
if (objHeaderMatcher.matches()) {
String object = objHeaderMatcher.group(2);
constructObject(chemFile.getBuilder(), object);
int id = Integer.parseInt(objHeaderMatcher.group(1));
line = readLine();
while (input.ready() && line != null && !(line.trim().equals(")"))) {
Matcher objCommandMatcher = objCommand.matcher(line);
objHeaderMatcher = objHeader.matcher(line);
if (objHeaderMatcher.matches()) {
object = objHeaderMatcher.group(2);
id = Integer.parseInt(objHeaderMatcher.group(1));
constructObject(chemFile.getBuilder(), object);
} else if (objCommandMatcher.matches()) {
String format = objCommandMatcher.group(1);
String command = objCommandMatcher.group(2);
String field = objCommandMatcher.group(3);
processModelCommand(object, command, format, field);
} else {
logger.warn("Skipping line: " + line);
}
line = readLine();
}
if (chemObject instanceof IAtom) {
atomids.put(id, modelStructure.getAtomCount());
atomGivenIds.put(Integer.valueOf((String) chemObject.getProperty(PMP_ID)), id);
modelStructure.addAtom((IAtom) chemObject);
} else if (chemObject instanceof IBond) {
} else {
logger.error("chemObject is not initialized or of bad class type");
}
}
line = readLine();
}
assert line != null;
if (line.startsWith("%%Model End")) {
int bondsFound = bondids.size();
logger.debug("Found #bonds: ", bondsFound);
logger.debug("#atom ones: ", bondAtomOnes.size());
logger.debug("#atom twos: ", bondAtomTwos.size());
logger.debug("#orders: ", bondOrders.size());
for (Integer index : bondids.keySet()) {
double order = (bondOrders.get(index) != null ? bondOrders.get(index) : 1.0);
logger.debug("index: ", index);
logger.debug("ones: ", bondAtomOnes.get(index));
IAtom atom1 = modelStructure.getAtom(atomids.get(bondAtomOnes.get(index)));
IAtom atom2 = modelStructure.getAtom(atomids.get(bondAtomTwos.get(index)));
IBond bond = modelStructure.getBuilder().newInstance(IBond.class, atom1, atom2);
if (order == 1.0) {
bond.setOrder(IBond.Order.SINGLE);
} else if (order == 2.0) {
bond.setOrder(IBond.Order.DOUBLE);
} else if (order == 3.0) {
bond.setOrder(IBond.Order.TRIPLE);
} else if (order == 4.0) {
bond.setOrder(IBond.Order.QUADRUPLE);
}
modelStructure.addBond(bond);
}
}
} else if (line.startsWith("%%Traj Start")) {
chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);
double energyFragment = 0.0;
double energyTotal = 0.0;
int Z = 1;
while (input.ready() && line != null && !(line.startsWith("%%Traj End"))) {
if (line.startsWith("%%Start Frame")) {
chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
crystal = chemFile.getBuilder().newInstance(ICrystal.class);
while (input.ready() && line != null && !(line.startsWith("%%End Frame"))) {
if (line.startsWith("%%Atom Coords")) {
if (energyFragment != 0.0 && energyTotal != 0.0) {
Z = (int) Math.round(energyTotal / energyFragment);
logger.debug("Z derived from energies: ", Z);
}
int expatoms = modelStructure.getAtomCount();
for (int molCount = 1; molCount <= Z; molCount++) {
IAtomContainer clone = modelStructure.getBuilder().newInstance(IAtomContainer.class);
for (int i = 0; i < expatoms; i++) {
line = readLine();
IAtom a = clone.getBuilder().newInstance(IAtom.class);
StringTokenizer st = new StringTokenizer(line, " ");
a.setPoint3d(new Point3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken())));
a.setCovalentRadius(0.6);
IAtom modelAtom = modelStructure.getAtom(atomids.get(atomGivenIds.get(i + 1)));
a.setSymbol(modelAtom.getSymbol());
clone.addAtom(a);
}
rebonder.rebond(clone);
crystal.add(clone);
}
} else if (line.startsWith("%%E/Frag")) {
line = readLine().trim();
energyFragment = Double.parseDouble(line);
} else if (line.startsWith("%%Tot E")) {
line = readLine().trim();
energyTotal = Double.parseDouble(line);
} else if (line.startsWith("%%Lat Vects")) {
StringTokenizer st;
line = readLine();
st = new StringTokenizer(line, " ");
crystal.setA(new Vector3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken())));
line = readLine();
st = new StringTokenizer(line, " ");
crystal.setB(new Vector3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken())));
line = readLine();
st = new StringTokenizer(line, " ");
crystal.setC(new Vector3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken())));
} else if (line.startsWith("%%Space Group")) {
line = readLine().trim();
if ("P 21 21 21 (1)".equals(line)) {
crystal.setSpaceGroup("P 2_1 2_1 2_1");
} else {
crystal.setSpaceGroup("P1");
}
}
line = readLine();
}
chemModel.setCrystal(crystal);
chemSequence.addChemModel(chemModel);
}
line = readLine();
}
chemFile.addChemSequence(chemSequence);
}
line = readLine();
}
} catch (IOException e) {
logger.error("An IOException happened: ", e.getMessage());
logger.debug(e);
chemFile = null;
} catch (CDKException e) {
logger.error("An CDKException happened: ", e.getMessage());
logger.debug(e);
chemFile = null;
}
return chemFile;
} | /storage/io/src/main/java/org/openscience/cdk/io/PMPReader.java |
robustness-copilot_data_705 | /**
* Destroys this entity by removing it from the world and marking it as not being active.
*/
public void remove(){
removed = true;
active = false;
boundingBox = null;
world.getEntityManager().unregister(this);
server.getEntityIdManager().deallocate(this);
this.setPassenger(null);
leaveVehicle();
ImmutableList.copyOf(this.leashedEntities).forEach(e -> unleash(e, UnleashReason.HOLDER_GONE));
if (isLeashed()) {
unleash(this, UnleashReason.HOLDER_GONE);
}
} | /src/main/java/net/glowstone/entity/GlowEntity.java |
robustness-copilot_data_706 | /**
* Obtain the permutation parity (-1,0,+1) to put the ligands in descending
* order (highest first). A parity of 0 indicates two or more ligands were
* equivalent.
*
* @param ligands the ligands to sort
* @return parity, odd (-1), even (+1) or none (0)
*/
private static int permParity(final ILigand[] ligands){
int swaps = 0;
for (int j = 1, hi = ligands.length; j < hi; j++) {
ILigand ligand = ligands[j];
int i = j - 1;
int cmp = 0;
while ((i >= 0) && (cmp = cipRule.compare(ligand, ligands[i])) > 0) {
ligands[i + 1] = ligands[i--];
swaps++;
}
if (cmp == 0)
return 0;
ligands[i + 1] = ligand;
}
return (swaps & 0x1) == 0x1 ? -1 : +1;
} | /descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java |
robustness-copilot_data_707 | /**
* Hydrogen atom types are assigned based on their parent types. The mmff-symb-mapping file
* provides this mapping.
*
* @param hdefIn input stream of mmff-symb-mapping.tsv
* @return mapping of parent to hydrogen definitions
* @throws IOException
*/
private Map<String, String> loadHydrogenDefinitions(InputStream hdefIn) throws IOException{
final Map<String, String> hdefs = new HashMap<String, String>(200);
BufferedReader br = new BufferedReader(new InputStreamReader(hdefIn));
br.readLine();
String line = null;
while ((line = br.readLine()) != null) {
String[] cols = line.split("\t");
hdefs.put(cols[0].trim(), cols[3].trim());
}
return hdefs;
} | /tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAtomTypeMatcher.java |
robustness-copilot_data_708 | /**
* Returns a map from appenders to levels for a logger.
* <p>
* The map contains the effective log levels, that is, the levels used for filtering log
* events.
*/
private synchronized Map<String, Level> computeEffectiveMap(LoggerName logger){
Map<String, Level> inheritedMap = getInheritedMap(logger);
if (!isRoot(logger)) {
LoggerName parent = logger.getParent();
if (parent != null) {
Map<String, Level> mergedMap = computeEffectiveMap(parent);
mergedMap.putAll(inheritedMap);
return mergedMap;
}
}
return inheritedMap;
} | /modules/cells/src/main/java/dmg/util/logback/FilterThresholdSet.java |
robustness-copilot_data_709 | /**
* Removes all isotopes from a given element in the MolecularFormula.
*
* @param formula IMolecularFormula molecularFormula
* @param element The IElement of the IIsotopes to be removed
* @return The molecularFormula with the isotopes removed
*/
public static IMolecularFormula removeElement(IMolecularFormula formula, IElement element){
for (IIsotope isotope : getIsotopes(formula, element)) {
formula.removeIsotope(isotope);
}
return formula;
} | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_710 | /**
* Adds or replaces a list subtag with a list of doubles.
*
* @param key the key to write to
* @param list the list contents as doubles, to convert to double tags
*/
public void putDoubleList(@NonNls String key, List<Double> list){
putList(key, TagType.DOUBLE, list, DoubleTag::new);
} | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_711 | /**
* True, if the MolecularFormula contains the given IIsotope object and not
* the instance. The method looks for other isotopes which has the same
* symbol, natural abundance and exact mass.
*
* @param isotope The IIsotope this MolecularFormula is searched for
* @return True, if the MolecularFormula contains the given isotope object
*/
public boolean contains(IIsotope isotope){
for (IIsotope thisIsotope : isotopes()) {
if (isTheSame(thisIsotope, isotope)) {
return true;
}
}
return false;
} | /base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java |
robustness-copilot_data_712 | /**
* Parses the pattern into a {@link NodeWriter}.
*
* @return a {@link NodeWriter}
* @throws JsonPatternException thrown in case of invalid pattern
*/
private NodeWriter<Event> initializeNodeWriter() throws JsonPatternException{
AbstractJsonPatternParser<Event> parser = createParser(this.jsonFactory);
parser.setOmitEmptyFields(omitEmptyFields);
return parser.parse(pattern);
} | /src/main/java/net/logstash/logback/composite/AbstractPatternJsonProvider.java |
robustness-copilot_data_713 | /**
* Method for constructing a new instance with configuration that
* updates passed Object (as root value), instead of constructing
* a new value.
*<p>
* Note that the method does NOT change state of this reader, but
* rather construct and returns a newly configured instance.
*/
public ObjectReader withValueToUpdate(Object value){
if (value == _valueToUpdate)
return this;
if (value == null) {
return _new(this, _config, _valueType, _rootDeserializer, null, _schema, _injectableValues, _dataFormatReaders);
}
JavaType t;
if (_valueType == null) {
t = _config.constructType(value.getClass());
} else {
t = _valueType;
}
return _new(this, _config, t, _rootDeserializer, value, _schema, _injectableValues, _dataFormatReaders);
} | /src/main/java/com/fasterxml/jackson/databind/ObjectReader.java |
robustness-copilot_data_714 | /**
* Returns a list of the vertices contained in this cycle.
* The vertices are in the order of a traversal of the cycle.
*
* @return a list of the vertices contained in this cycle
*/
public List vertexList(){
List vertices = new ArrayList(edgeSet().size());
Object startVertex = vertexSet().iterator().next();
Object vertex = startVertex;
Object previousVertex = null;
Object nextVertex = null;
while (nextVertex != startVertex) {
assert (degreeOf(vertex) == 2);
List edges = edgesOf(vertex);
vertices.add(vertex);
Edge edge = (Edge) edges.get(0);
nextVertex = edge.oppositeVertex(vertex);
if (nextVertex == previousVertex) {
edge = (Edge) edges.get(1);
nextVertex = edge.oppositeVertex(vertex);
}
previousVertex = vertex;
vertex = nextVertex;
}
return vertices;
} | /legacy/src/main/java/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycle.java |
robustness-copilot_data_715 | /**
* Create the oak index based on the ensure definition.
*
* @param ensuredDefinition the ensure definition
* @param oakIndexes the parent oak index folder
* @return the updated oak index resource
* @throws PersistenceException
* @throws RepositoryException
*/
public Resource create(@Nonnull final Resource ensuredDefinition, @Nonnull final Resource oakIndexes) throws RepositoryException{
final Node oakIndex = JcrUtil.copy(ensuredDefinition.adaptTo(Node.class), oakIndexes.adaptTo(Node.class), ensuredDefinition.getName());
oakIndex.setPrimaryType(NT_OAK_QUERY_INDEX_DEFINITION);
oakIndex.setProperty(JcrConstants.JCR_CREATED, Calendar.getInstance());
oakIndex.setProperty(JcrConstants.JCR_CREATED_BY, ENSURE_OAK_INDEX_USER_NAME);
log.info("Created Oak Index at [ {} ] with Ensure Definition [ {} ]", oakIndex.getPath(), ensuredDefinition.getPath());
return ensuredDefinition.getResourceResolver().getResource(oakIndex.getPath());
} | /bundle/src/main/java/com/adobe/acs/commons/oak/impl/EnsureOakIndexJobHandler.java |
robustness-copilot_data_716 | /**
* Test a permutation to see if it is in the group. Note that this also
* alters the permutation passed in.
*
* @param permutation the one to test
* @return the position it should be in the group, if any
*/
public int test(Permutation permutation){
for (int i = 0; i < size; i++) {
int x = permutation.get(base.get(i));
Permutation h = permutations[i][x];
if (h == null) {
return i;
} else {
permutation.setTo(h.invert().multiply(permutation));
}
}
return size;
} | /tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java |
robustness-copilot_data_717 | /**
* Create a {@link CoordinatorRegistryCenter} or return the existing one if there is one set up with the same {@code connectionString}, {@code namespace} and {@code digest} already.
*
* @param connectString registry center connect string
* @param namespace registry center namespace
* @param digest registry center digest
* @return registry center
*/
public static CoordinatorRegistryCenter createCoordinatorRegistryCenter(final String connectString, final String namespace, final String digest){
Hasher hasher = Hashing.sha256().newHasher().putString(connectString, StandardCharsets.UTF_8).putString(namespace, StandardCharsets.UTF_8);
if (!Strings.isNullOrEmpty(digest)) {
hasher.putString(digest, StandardCharsets.UTF_8);
}
HashCode hashCode = hasher.hash();
return REG_CENTER_REGISTRY.computeIfAbsent(hashCode, unused -> {
CoordinatorRegistryCenter result = newCoordinatorRegistryCenter(connectString, namespace, digest);
result.init();
return result;
});
} | /elasticjob-lite/elasticjob-lite-lifecycle/src/main/java/org/apache/shardingsphere/elasticjob/lite/lifecycle/internal/reg/RegistryCenterFactory.java |
robustness-copilot_data_718 | /**
* Build a new StatePath that points to the same location from the immediate child's
* point-of-view. For example, if the current path is characterised as <tt>aa.bb.cc</tt>, then
* the returned StatePath is characterised by <tt>bb.cc</tt>.
* <p>
* If the path has no children of children, null is returned.
*
* @return the path for the child element, or null if there is no child.
*/
public StatePath childPath(){
if (_elements == null || _elements.size() <= 1) {
return null;
}
return new StatePath(_elements.subList(1, _elements.size()), _elements.size() - 1);
} | /modules/dcache-info/src/main/java/org/dcache/services/info/base/StatePath.java |
robustness-copilot_data_719 | /**
* Create a dynamic server config using server template and index number of this server.
*
* @param name Name of the server
* @param index index of this server within the cluster, for example, the index of dserver-2 would
* be 2
* @param clusterName name of the WLS cluster that this server belongs to
* @param domainName name of the WLS domain that this server belongs to
* @param calculatedListenPorts whether listen ports are calculated according to configuration in
* the dynamic cluster
* @param serverTemplate server template used for servers in the dynamic cluster
* @return a dynamic server configuration object containing configuration of this dynamic server
*/
static WlsDynamicServerConfig create(String name, int index, String clusterName, String domainName, boolean calculatedListenPorts, WlsServerConfig serverTemplate){
Integer listenPort = serverTemplate.getListenPort();
Integer sslListenPort = serverTemplate.getSslListenPort();
List<NetworkAccessPoint> networkAccessPoints = new ArrayList<>();
if (serverTemplate.getNetworkAccessPoints() != null) {
for (NetworkAccessPoint networkAccessPoint : serverTemplate.getNetworkAccessPoints()) {
Integer networkAccessPointListenPort = networkAccessPoint.getListenPort();
if (calculatedListenPorts) {
networkAccessPointListenPort = networkAccessPointListenPort == null ? (DEFAULT_NAP_LISTEN_PORT_RANGE_BASE + index) : networkAccessPointListenPort + index;
}
networkAccessPoints.add(new NetworkAccessPoint(networkAccessPoint.getName(), networkAccessPoint.getProtocol(), networkAccessPointListenPort, networkAccessPoint.getPublicPort()));
}
}
// calculate listen ports if configured to do so
if (calculatedListenPorts) {
listenPort = (listenPort == null) ? (DEFAULT_LISTEN_PORT_RANGE_BASE + index) : (listenPort + index);
sslListenPort = (sslListenPort == null) ? (DEFAULT_SSL_LISTEN_PORT_RANGE_BASE + index) : (sslListenPort + index);
}
MacroSubstitutor macroSubstitutor = new MacroSubstitutor(index, name, clusterName, domainName, serverTemplate.getMachineName());
return new WlsDynamicServerConfig(name, listenPort, macroSubstitutor.substituteMacro(serverTemplate.getListenAddress()), sslListenPort, macroSubstitutor.substituteMacro(serverTemplate.getMachineName()), serverTemplate.getAdminPort(), networkAccessPoints);
} | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsDynamicServerConfig.java |
robustness-copilot_data_720 | /**
* For links with unknown max speed we assume that links with a length of less than 300m are urban links. For urban
* links with a length of 0m the speed is 10km/h. For links with a length of 300m the speed is the default freespeed
* property for that highway type. For links with a length between 0 and 300m the speed is interpolated linearly.
* (2.778m/s ~ 10km/h)
*
* All links longer than 300m the default freesped property is assumed
*/
public static double calculateSpeedIfNoSpeedTag(double linkLength, LinkProperties properties){
if (properties.hierarchyLevel > LinkProperties.LEVEL_MOTORWAY && properties.hierarchyLevel <= LinkProperties.LEVEL_TERTIARY && linkLength <= 300) {
return ((2.7778 + (properties.freespeed - 2.7778) / 300 * linkLength));
}
return properties.freespeed;
} | /contribs/osm/src/main/java/org/matsim/contrib/osm/networkReader/LinkProperties.java |
robustness-copilot_data_721 | /**
* This function takes a path and tries to find the file in the file system or
* in the resource path. The order of resolution is as follows:
*
* <ol>
* <li>Find path in file system</li>
* <li>Find path in file system with compression extension (e.g. *.gz)</li>
* <li>Find path in class path as resource</li>
* <li>Find path in class path with compression extension</li>
* </ol>
*
* In case the filename is a URL (i.e. starting with "file:" or "jar:file:"),
* then no resolution is done but the provided filename returned as URL.
*
* @throws UncheckedIOException
*/
public static URL resolveFileOrResource(String filename) throws UncheckedIOException{
try {
// I) do not handle URLs
if (filename.startsWith("jar:file:") || filename.startsWith("file:") || filename.startsWith("https:")) {
// looks like an URI
return new URL(filename);
}
// II) Replace home identifier
if (filename.startsWith("~" + File.separator)) {
filename = System.getProperty("user.home") + filename.substring(1);
}
// III.1) First, try to find the file in the file system
File file = new File(filename);
if (file.exists()) {
logger.info(String.format("Resolved %s to %s", filename, file));
return file.toURI().toURL();
}
// III.2) Try to find file with an additional postfix for compression
for (String postfix : COMPRESSION_EXTENSIONS.keySet()) {
file = new File(filename + "." + postfix);
if (file.exists()) {
logger.info(String.format("Resolved %s to %s", filename, file));
return file.toURI().toURL();
}
}
// IV.1) First, try to find the file in the class path
URL resource = IOUtils.class.getClassLoader().getResource(filename);
if (resource != null) {
logger.info(String.format("Resolved %s to %s", filename, resource));
return resource;
}
// IV.2) Second, try to find the resource with a compression extension
for (String postfix : COMPRESSION_EXTENSIONS.keySet()) {
resource = IOUtils.class.getClassLoader().getResource(filename + "." + postfix);
if (resource != null) {
logger.info(String.format("Resolved %s to %s", filename, resource));
return resource;
}
}
throw new FileNotFoundException(filename);
} catch (FileNotFoundException | MalformedURLException e) {
throw new UncheckedIOException(e);
}
} | /matsim/src/main/java/org/matsim/core/utils/io/IOUtils.java |
robustness-copilot_data_722 | /**
* Adds a Molecule to the list of templates use by this TemplateHandler.
*
* @param molecule The molecule to be added to the TemplateHandler
*/
public void addMolecule(IAtomContainer molecule){
if (!GeometryUtil.has2DCoordinates(molecule))
throw new IllegalArgumentException("Template did not have 2D coordinates");
GeometryUtil.scaleMolecule(molecule, GeometryUtil.getScaleFactor(molecule, StructureDiagramGenerator.DEFAULT_BOND_LENGTH));
templates.add(molecule);
anonPatterns.add(VentoFoggia.findSubstructure(molecule, anonAtomMatcher, anonBondMatcher));
elemPatterns.add(VentoFoggia.findSubstructure(molecule, elemAtomMatcher, anonBondMatcher));
} | /tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java |
robustness-copilot_data_723 | /**
* Return true if the specified 'schema' is an object that can be extended with additional properties.
* Additional properties means a Schema should support all explicitly defined properties plus any
* undeclared properties.
*
* A MapSchema differs from an ObjectSchema in the following way:
* - An ObjectSchema is not extensible, i.e. it has a fixed number of properties.
* - A MapSchema is an object that can be extended with an arbitrary set of properties.
* The payload may include dynamic properties.
*
* Note that isMapSchema returns true for a composed schema (allOf, anyOf, oneOf) that also defines
* additionalproperties.
*
* For example, an OpenAPI schema is considered a MapSchema in the following scenarios:
*
* type: object
* additionalProperties: true
*
* type: object
* additionalProperties:
* type: object
* properties:
* code:
* type: integer
*
* allOf:
* - $ref: '#/components/schemas/Class1'
* - $ref: '#/components/schemas/Class2'
* additionalProperties: true
*
* @param schema the OAS schema
* @return true if the specified schema is a Map schema.
*/
public static boolean isMapSchema(Schema schema){
if (schema instanceof MapSchema) {
return true;
}
if (schema == null) {
return false;
}
if (schema.getAdditionalProperties() instanceof Schema) {
return true;
}
if (schema.getAdditionalProperties() instanceof Boolean && (Boolean) schema.getAdditionalProperties()) {
return true;
}
return false;
} | /modules/openapi-generator/src/main/java/org/openapitools/codegen/utils/ModelUtils.java |
robustness-copilot_data_724 | /**
* Sort the {@code indices}, which correspond to an index in the {@code atoms} array in
* clockwise order.
*
* @param indices indices, 0 to n
* @param focus the central atom
* @param atoms the neighbors of the focus
* @param n the number of neighbors
* @return the permutation parity of the sort
*/
private int sortClockwise(int[] indices, IAtom focus, IAtom[] atoms, int n){
int x = 0;
for (int j = 1; j < n; j++) {
int v = indices[j];
int i = j - 1;
while ((i >= 0) && less(v, indices[i], atoms, focus.getPoint2d())) {
indices[i + 1] = indices[i--];
x++;
}
indices[i + 1] = v;
}
return indexParity(x);
} | /tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java |
robustness-copilot_data_725 | /**
* Open a regular property file (not embedded in a resource - use {@link #parseDefaultPropertyFileFromResource}
* for that) and parse it.
*
* @param potentialPropertyFile path and file name to the the property file
* @throws IOException if the file cannot be opened
* @throws CommandLineParsingException if an error occurs during parsing
*/
private void parseDefaultPropertyFileFromFile(File potentialPropertyFile) throws IOException, CommandLineParsingException{
try (FileInputStream stream = new FileInputStream(potentialPropertyFile)) {
parsePropertiesFile(stream);
}
} | /liquibase-core/src/main/java/liquibase/integration/commandline/Main.java |
robustness-copilot_data_726 | /**
* Inserts the given Node n into the pendingNodes queue and updates its time and cost information.
*
* @param n The Node that is revisited.
* @param data The data for node.
* @param pendingNodes The nodes visited and not processed yet.
* @param time The time of the visit of n.
* @param cost The accumulated cost at the time of the visit of n.
* @param expectedRemainingCost The expected remaining travel cost when
* traveling from n to the target node of the route.
* @param outLink The link from which we came visiting n.
*/
private void visitNode(final Node n, final AStarNodeData data, final RouterPriorityQueue<Node> pendingNodes, final double time, final double cost, final double expectedRemainingCost, final Link outLink){
data.setExpectedRemainingCost(expectedRemainingCost);
super.visitNode(n, data, pendingNodes, time, cost, outLink);
} | /matsim/src/main/java/org/matsim/core/router/AStarEuclidean.java |
robustness-copilot_data_727 | /**
* Find a specific mail domain group by it's alias.
* @param groupAlias
* @return
*/
Optional<MailDomainGroup> findByAlias(String groupAlias){
try {
return Optional.of(em.createNamedQuery("MailDomainGroup.findByPersistedGroupAlias", MailDomainGroup.class).setParameter("persistedGroupAlias", groupAlias).getSingleResult());
} catch (NoResultException nre) {
return Optional.empty();
}
} | /src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroupServiceBean.java |
robustness-copilot_data_728 | /**
* Adds a {@link MetricRegistryListener} to a collection of listeners that will be notified on
* metric creation. Listeners will be notified in the order in which they are added.
* <p>
* <b>N.B.:</b> The listener will be notified of all existing metrics when it first registers.
*
* @param listener the listener that will be notified
*/
public void addListener(MetricRegistryListener listener){
listeners.add(listener);
for (Map.Entry<MetricName, Metric> entry : metrics.entrySet()) {
notifyListenerOfAddedMetric(listener, entry.getValue(), entry.getKey());
}
} | /metrics-core/src/main/java/io/dropwizard/metrics5/MetricRegistry.java |
robustness-copilot_data_729 | /**
* Removes a particular monomer, specified by its name.
*
* @param name The name of the monomer to remove
*/
public void removeMonomer(String name){
if (monomers.containsKey(name)) {
Monomer monomer = (Monomer) monomers.get(name);
this.remove(monomer);
monomers.remove(name);
}
} | /base/data/src/main/java/org/openscience/cdk/Polymer.java |
robustness-copilot_data_730 | /**
* Calculates the number of bits that would be needed to store the given value.
*
* @param number the value
* @return The number of bits that would be needed to store the value.
*/
public static int calculateNeededBits(int number){
int count = 0;
do {
count++;
number >>>= 1;
} while (number != 0);
return count;
} | /src/main/java/net/glowstone/util/VariableValueArray.java |
robustness-copilot_data_731 | /**
* Returns an iterator over the elements in this queue. The iterator
* does not return the elements in any particular order. Removing
* elements is not supported via the iterator.
*
* @return an iterator over the elements in this queue.
*/
public Iterator<E> iterator(){
return new Iterator<E>() {
final Iterator<E> iterDelegate = PseudoRemovePriorityQueue.this.lastEntry.keySet().iterator();
@Override
public boolean hasNext() {
return this.iterDelegate.hasNext();
}
@Override
public E next() {
return this.iterDelegate.next();
}
@Override
public void remove() {
throw new UnsupportedOperationException();
}
};
} | /matsim/src/main/java/org/matsim/core/utils/collections/PseudoRemovePriorityQueue.java |
robustness-copilot_data_732 | /**
* Create a CompletableFuture from guava's ListenableFuture to help migration from Guava to
* Java8.
*
* @param listenable ListenableFuture to convert.
* @return new CompletableFuture.
*/
public static CompletableFuture<T> fromListenableFuture(ListenableFuture<T> listenable){
final CompletableFuture<T> completable = new CompletableFuture<T>() {
@Override
public boolean cancel(boolean mayInterruptIfRunning) {
boolean result = listenable.cancel(mayInterruptIfRunning);
super.cancel(mayInterruptIfRunning);
return result;
}
};
Futures.addCallback(listenable, new FutureCallback<T>() {
@Override
public void onSuccess(T result) {
completable.complete(result);
}
@Override
public void onFailure(Throwable t) {
completable.completeExceptionally(t);
}
}, MoreExecutors.directExecutor());
return completable;
} | /modules/common/src/main/java/org/dcache/util/CompletableFutures.java |
robustness-copilot_data_733 | /**
* Check if all atoms in the bond list have 2D coordinates. There is some
* redundant checking but the list will typically be short.
*
* @param bonds the bonds to check
* @return whether all atoms have 2D coordinates
*/
private static boolean has2DCoordinates(List<IBond> bonds){
for (IBond bond : bonds) {
if (bond.getBegin().getPoint2d() == null || bond.getEnd().getPoint2d() == null)
return false;
}
return true;
} | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricCumulativeDoubleBondFactory.java |
robustness-copilot_data_734 | /**
* Shift the container horizontally to the right to make its bounds not
* overlap with the other bounds.
*
* @param container the {@link IAtomContainer} to shift to the right
* @param bounds the {@link Rectangle2D} of the {@link IAtomContainer}
* to shift
* @param last the bounds that is used as reference
* @param gap the gap between the two {@link Rectangle2D}s
* @return the {@link Rectangle2D} of the {@link IAtomContainer}
* after the shift
*/
public static Rectangle2D shiftContainer(IAtomContainer container, Rectangle2D bounds, Rectangle2D last, double gap){
if (last.getMaxX() + gap >= bounds.getMinX()) {
double xShift = last.getMaxX() + gap - bounds.getMinX();
Vector2d shift = new Vector2d(xShift, 0.0);
GeometryTools.translate2D(container, shift);
return new Rectangle2D.Double(bounds.getX() + xShift, bounds.getY(), bounds.getWidth(), bounds.getHeight());
} else {
return bounds;
}
} | /legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java |
robustness-copilot_data_735 | /**
* Returns true if another {@link IAtomContainer} can be read.
*/
public boolean hasNext(){
if (nextAvailableIsKnown) {
return hasNext;
}
hasNext = false;
nextMolecule = null;
try {
currentFormat = (IChemFormat) MDLFormat.getInstance();
int lineNum = 0;
buffer.setLength(0);
while ((currentLine = input.readLine()) != null) {
buffer.append(currentLine).append(LINE_SEPARATOR);
lineNum++;
if (lineNum == 4) {
Matcher versionMatcher = MDL_VERSION.matcher(currentLine);
if (versionMatcher.find()) {
currentFormat = "2000".equals(versionMatcher.group(1)) ? (IChemFormat) MDLV2000Format.getInstance() : (IChemFormat) MDLV3000Format.getInstance();
}
}
if (currentLine.startsWith(M_END)) {
logger.debug("MDL file part read: ", buffer);
IAtomContainer molecule = null;
try {
ISimpleChemObjectReader reader = getReader(currentFormat);
reader.setReader(new StringReader(buffer.toString()));
molecule = reader.read(builder.newAtomContainer());
} catch (Exception exception) {
logger.error("Error while reading next molecule: " + exception.getMessage());
logger.debug(exception);
}
if (molecule != null) {
readDataBlockInto(molecule);
hasNext = true;
nextAvailableIsKnown = true;
nextMolecule = molecule;
return true;
} else if (skip) {
String line;
while ((line = input.readLine()) != null) {
if (line.startsWith(SDF_RECORD_SEPARATOR)) {
break;
}
}
} else {
return false;
}
buffer.setLength(0);
lineNum = 0;
}
if (currentLine.startsWith(SDF_RECORD_SEPARATOR)) {
buffer.setLength(0);
lineNum = 0;
}
}
} catch (IOException exception) {
logger.error("Error while reading next molecule: " + exception.getMessage());
logger.debug(exception);
}
return false;
} | /storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java |
robustness-copilot_data_736 | /**
* Positions an outline in the subscript position relative to another 'primary' label.
*
* @param label a label outline
* @param subscript the label outline to position as subscript
* @return positioned subscript outline
*/
TextOutline positionSubscript(TextOutline label, TextOutline subscript){
final Rectangle2D hydrogenBounds = label.getBounds();
final Rectangle2D hydrogenCountBounds = subscript.getBounds();
subscript = subscript.translate((hydrogenBounds.getMaxX() + padding) - hydrogenCountBounds.getMinX(), (hydrogenBounds.getMaxY() + (hydrogenCountBounds.getHeight() / 2)) - hydrogenCountBounds.getMaxY());
return subscript;
} | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java |
robustness-copilot_data_737 | /**
* Find an r such that this[r] != other[r].
* @param other the other permutation to compare with
* @return the first point at which the two permutations differ
*/
public int firstIndexOfDifference(Permutation other){
int r = 0;
while ((r < values.length) && values[r] == other.get(r)) {
r++;
}
return r;
} | /tool/group/src/main/java/org/openscience/cdk/group/Permutation.java |
robustness-copilot_data_738 | /**
* IntIterator of source table row numbers that are present in this view. This can be used to in
* combination with the source table to iterate over the cells of a column in a sorted order
* without copying the column.
*
* @return an int iterator of row numbers in the source table that are present in this view.
*/
protected PrimitiveIterator.OfInt sourceRowNumberIterator(){
if (this.isSorted()) {
return Arrays.stream(sortOrder).iterator();
} else if (this.hasSelection()) {
return selection.iterator();
}
return Selection.withRange(0, table.rowCount()).iterator();
} | /core/src/main/java/tech/tablesaw/table/TableSlice.java |
robustness-copilot_data_739 | /**
* Apply the MDL valence model to the provided atom container.
*
* @param container an atom container loaded from an MDL format
* @return the container (for convenience)
*/
static IAtomContainer apply(IAtomContainer container){
int n = container.getAtomCount();
int[] valences = new int[n];
Map<IAtom, Integer> atomToIndex = new HashMap<>(2 * n);
for (IAtom atom : container.atoms()) atomToIndex.put(atom, atomToIndex.size());
// compute the bond order sums
for (IBond bond : container.bonds()) {
int u = atomToIndex.get(bond.getBegin());
int v = atomToIndex.get(bond.getEnd());
int bondOrder = bond.getOrder().numeric();
valences[u] += bondOrder;
valences[v] += bondOrder;
}
for (int i = 0; i < n; i++) {
IAtom atom = container.getAtom(i);
Integer charge = atom.getFormalCharge();
Integer element = atom.getAtomicNumber();
if (element == null)
continue;
// unset = 0 in this case
charge = charge == null ? 0 : charge;
int explicit = valences[i];
// if there was a valence read from the mol file use that otherwise
// use the default value from the valence model to set the correct
// number of implied hydrogens
if (atom.getValency() != null) {
atom.setImplicitHydrogenCount(atom.getValency() - explicit);
} else {
int implicit = implicitValence(element, charge, valences[i]);
atom.setImplicitHydrogenCount(implicit - explicit);
atom.setValency(implicit);
}
}
return container;
} | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLValence.java |
robustness-copilot_data_740 | /**
* Choose any possible quadruple of the set of atoms
* in ac and establish all of the possible bonding schemes according to
* Faulon's equations.
*/
public static List<IAtomContainer> sample(IAtomContainer ac){
LOGGER.debug("RandomGenerator->mutate() Start");
List<IAtomContainer> structures = new ArrayList<IAtomContainer>();
int nrOfAtoms = ac.getAtomCount();
double a11 = 0, a12 = 0, a22 = 0, a21 = 0;
double b11 = 0, lowerborder = 0, upperborder = 0;
double b12 = 0;
double b21 = 0;
double b22 = 0;
double[] cmax = new double[4];
double[] cmin = new double[4];
IAtomContainer newAc = null;
IAtom ax1 = null, ax2 = null, ay1 = null, ay2 = null;
IBond b1 = null, b2 = null, b3 = null, b4 = null;
// int[] choices = new int[3];
/* We need at least two non-zero bonds in order to be successful */
int nonZeroBondsCounter = 0;
for (int x1 = 0; x1 < nrOfAtoms; x1++) {
for (int x2 = x1 + 1; x2 < nrOfAtoms; x2++) {
for (int y1 = x2 + 1; y1 < nrOfAtoms; y1++) {
for (int y2 = y1 + 1; y2 < nrOfAtoms; y2++) {
nonZeroBondsCounter = 0;
ax1 = ac.getAtom(x1);
ay1 = ac.getAtom(y1);
ax2 = ac.getAtom(x2);
ay2 = ac.getAtom(y2);
/* Get four bonds for these four atoms */
b1 = ac.getBond(ax1, ay1);
if (b1 != null) {
a11 = BondManipulator.destroyBondOrder(b1.getOrder());
nonZeroBondsCounter++;
} else {
a11 = 0;
}
b2 = ac.getBond(ax1, ay2);
if (b2 != null) {
a12 = BondManipulator.destroyBondOrder(b2.getOrder());
nonZeroBondsCounter++;
} else {
a12 = 0;
}
b3 = ac.getBond(ax2, ay1);
if (b3 != null) {
a21 = BondManipulator.destroyBondOrder(b3.getOrder());
nonZeroBondsCounter++;
} else {
a21 = 0;
}
b4 = ac.getBond(ax2, ay2);
if (b4 != null) {
a22 = BondManipulator.destroyBondOrder(b4.getOrder());
nonZeroBondsCounter++;
} else {
a22 = 0;
}
if (nonZeroBondsCounter > 1) {
/*
* Compute the range for b11 (see Faulons formulae
* for details)
*/
cmax[0] = 0;
cmax[1] = a11 - a22;
cmax[2] = a11 + a12 - 3;
cmax[3] = a11 + a21 - 3;
cmin[0] = 3;
cmin[1] = a11 + a12;
cmin[2] = a11 + a21;
cmin[3] = a11 - a22 + 3;
lowerborder = MathTools.max(cmax);
upperborder = MathTools.min(cmin);
for (b11 = lowerborder; b11 <= upperborder; b11++) {
if (b11 != a11) {
b12 = a11 + a12 - b11;
b21 = a11 + a21 - b11;
b22 = a22 - a11 + b11;
LOGGER.debug("Trying atom combination : " + x1 + ":" + x2 + ":" + y1 + ":" + y2);
try {
newAc = (IAtomContainer) ac.clone();
change(newAc, x1, y1, x2, y2, b11, b12, b21, b22);
if (ConnectivityChecker.isConnected(newAc)) {
structures.add(newAc);
} else {
LOGGER.debug("not connected");
}
} catch (CloneNotSupportedException e) {
LOGGER.error("Cloning exception: " + e.getMessage());
LOGGER.debug(e);
}
}
}
}
}
}
}
}
return structures;
} | /tool/structgen/src/main/java/org/openscience/cdk/structgen/VicinitySampler.java |
robustness-copilot_data_741 | /**
* Helper method that locates an atom based on its InChI atom table
* position, which has been set as ID.
* @param container input container
* @param position InChI atom table position
* @return atom on the position
*/
private IAtom findAtomByPosition(IAtomContainer container, int position){
String pos = String.valueOf(position);
for (IAtom atom : container.atoms()) {
if (atom.getID().equals(pos))
return atom;
}
return null;
} | /tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java |
robustness-copilot_data_742 | /**
* generate the order of the Elements according probability occurrence.,
* beginning the C, H, O, N, Si, P, S, F, Cl, Br, I, Sn, B, Pb, Tl, Ba, In, Pd,
* Pt, Os, Ag, Zr, Se, Zn, Cu, Ni, Co, Fe, Cr, Ti, Ca, K, Al, Mg, Na, Ce,
* Hg, Au, Ir, Re, W, Ta, Hf, Lu, Yb, Tm, Er, Ho, Dy, Tb, Gd, Eu, Sm, Pm,
* Nd, Pr, La, Cs, Xe, Te, Sb, Cd, Rh, Ru, Tc, Mo, Nb, Y, Sr, Rb, Kr, As,
* Ge, Ga, Mn, V, Sc, Ar, Ne, Be, Li, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac,
* Th, Pa, U, Np, Pu.
*
* @return Array with the elements ordered.
*
*/
private String[] generateOrderE(){
String[] listElements = new String[] { "C", "H", "O", "N", "Si", "P", "S", "F", "Cl", "Br", "I", "Sn", "B", "Pb", "Tl", "Ba", "In", "Pd", "Pt", "Os", "Ag", "Zr", "Se", "Zn", "Cu", "Ni", "Co", "Fe", "Cr", "Ti", "Ca", "K", "Al", "Mg", "Na", "Ce", "Hg", "Au", "Ir", "Re", "W", "Ta", "Hf", "Lu", "Yb", "Tm", "Er", "Ho", "Dy", "Tb", "Gd", "Eu", "Sm", "Pm", "Nd", "Pr", "La", "Cs", "Xe", "Te", "Sb", "Cd", "Rh", "Ru", "Tc", "Mo", "Nb", "Y", "Sr", "Rb", "Kr", "As", "Ge", "Ga", "Mn", "V", "Sc", "Ar", "Ne", "Be", "Li", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu" };
return listElements;
} | /legacy/src/main/java/org/openscience/cdk/formula/MassToFormulaTool.java |
robustness-copilot_data_743 | /**
* the method take a boolean checkAromaticity: if the boolean is true, it means that
* aromaticity has to be checked.
*
*@param mol AtomContainer for which this descriptor is to be calculated
*@return The number of failures of the Lipinski rule
*/
public DescriptorValue calculate(IAtomContainer mol){
mol = clone(mol);
int lipinskifailures = 0;
IMolecularDescriptor xlogP = new XLogPDescriptor();
Object[] xlogPparams = { checkAromaticity, Boolean.TRUE };
try {
xlogP.setParameters(xlogPparams);
double xlogPvalue = ((DoubleResult) xlogP.calculate(mol).getValue()).doubleValue();
IMolecularDescriptor acc = new HBondAcceptorCountDescriptor();
Object[] hBondparams = { checkAromaticity };
acc.setParameters(hBondparams);
int acceptors = ((IntegerResult) acc.calculate(mol).getValue()).intValue();
IMolecularDescriptor don = new HBondDonorCountDescriptor();
don.setParameters(hBondparams);
int donors = ((IntegerResult) don.calculate(mol).getValue()).intValue();
IMolecularDescriptor mw = new WeightDescriptor();
Object[] mwparams = { "*" };
mw.setParameters(mwparams);
double mwvalue = ((DoubleResult) mw.calculate(mol).getValue()).doubleValue();
IMolecularDescriptor rotata = new RotatableBondsCountDescriptor();
Object[] rotatableBondsParams = { false, true };
rotata.setParameters(rotatableBondsParams);
int rotatablebonds = ((IntegerResult) rotata.calculate(mol).getValue()).intValue();
if (xlogPvalue > 5.0) {
lipinskifailures += 1;
}
if (acceptors > 10) {
lipinskifailures += 1;
}
if (donors > 5) {
lipinskifailures += 1;
}
if (mwvalue > 500.0) {
lipinskifailures += 1;
}
if (rotatablebonds > 10.0) {
lipinskifailures += 1;
}
} catch (CDKException e) {
new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult((int) Double.NaN), getDescriptorNames(), e);
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(lipinskifailures), getDescriptorNames());
} | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java |
robustness-copilot_data_744 | /**
* Get the collection of task statistics in the most recent week.
*
* @return Collection of running task statistics data objects
*/
public List<TaskRunningStatistics> findTaskRunningStatisticsWeekly(){
if (!isRdbConfigured()) {
return Collections.emptyList();
}
return rdbRepository.findTaskRunningStatistics(StatisticTimeUtils.getStatisticTime(StatisticInterval.DAY, -7));
} | /elasticjob-cloud/elasticjob-cloud-scheduler/src/main/java/org/apache/shardingsphere/elasticjob/cloud/scheduler/statistics/StatisticManager.java |
robustness-copilot_data_745 | /**
* Pop a ZFrame and return the toString() representation of it.
*
* @return toString version of pop'ed frame, or null if no frame exists.
*/
public String popString(){
ZFrame frame = pop();
if (frame == null) {
return null;
}
return frame.toString();
} | /src/main/java/org/zeromq/ZMsg.java |
robustness-copilot_data_746 | /**
* Applies the given function to a list subtag if it is present and its contents are float
* tags.
*
* @param key the key to look up
* @param consumer the function to apply
* @return true if the tag exists and was passed to the consumer; false otherwise
*/
public boolean readFloatList(@NonNls String key, Consumer<? super List<Float>> consumer){
return readList(key, TagType.FLOAT, consumer);
} | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_747 | /**
* Evaluate the square of the Euclidean distance between two atoms.
*
*@param atom1 first atom
*@param atom2 second atom
*@return squared distance between the 2 atoms
*/
private double calculateSquaredDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2){
double distance = 0;
double tmp = 0;
Point3d firstPoint = atom1.getPoint3d();
Point3d secondPoint = atom2.getPoint3d();
tmp = firstPoint.distance(secondPoint);
distance = tmp * tmp;
return distance;
} | /tool/charges/src/main/java/org/openscience/cdk/charges/InductivePartialCharges.java |
robustness-copilot_data_748 | /**
* Reverse a list of tokens for display, flipping
* brackets as needed.
*
* @param tokens list of tokens
*/
static void reverse(List<String> tokens){
Collections.reverse(tokens);
Deque<String> numbers = new ArrayDeque<>();
for (int i = 0; i < tokens.size(); i++) {
String token = tokens.get(i);
if (token.equals("(")) {
tokens.set(i, ")");
String num = numbers.pop();
if (!num.isEmpty()) {
tokens.add(i + 1, num);
i++;
}
} else if (token.equals(")")) {
tokens.set(i, "(");
if (i > 0 && isNumber(tokens.get(i - 1))) {
numbers.push(tokens.remove(i - 1));
i--;
} else {
numbers.push("");
}
}
}
} | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java |
robustness-copilot_data_749 | /**
* Returns a string representation of the object: XML/UTF-8 encoded.
*
* @return object XML encoded
*/
public String toString(){
var stream = new ByteArrayOutputStream();
save(stream);
return stream.toString(StandardCharsets.UTF_8);
} | /cxx-squid/src/main/java/org/sonar/cxx/config/CxxSquidConfiguration.java |
robustness-copilot_data_750 | /**
* Use this fiber's executor to schedule an operation for some time in the future.
* @param timeout the interval before the check should run, in units
* @param unit the unit of time that defines the interval
* @param runnable the operation to run
*/
public void scheduleOnce(long timeout, TimeUnit unit, Runnable runnable){
this.owner.getExecutor().schedule(runnable, timeout, unit);
} | /operator/src/main/java/oracle/kubernetes/operator/work/Fiber.java |
robustness-copilot_data_751 | /**
* A line is skipped if it is empty or is a comment. MMFF files use '*' to mark comments and '$'
* for end of file.
*
* @param line an input line
* @return whether to skip this line
*/
private static boolean skipLine(String line){
return line.isEmpty() || line.charAt(0) == '*' || line.charAt(0) == '$';
} | /tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAtomTypeMatcher.java |
robustness-copilot_data_752 | /**
* Normalize a path by removing consecutive <code>/</code>(slashes).
*
* @param path Path to process.
* @return Safe path pattern.
*/
static String normalizePath(@Nullable String path){
if (path == null || path.length() == 0 || path.equals("/")) {
return "/";
}
int len = path.length();
boolean modified = false;
int p = 0;
char[] buff = new char[len + 1];
if (path.charAt(0) != '/') {
buff[p++] = '/';
modified = true;
}
for (int i = 0; i < path.length(); i++) {
char ch = path.charAt(i);
if (ch != '/') {
buff[p++] = ch;
} else if (i == 0 || path.charAt(i - 1) != '/') {
buff[p++] = ch;
} else {
modified = true;
}
}
return modified ? new String(buff, 0, p) : path;
} | /jooby/src/main/java/io/jooby/Router.java |
robustness-copilot_data_753 | /**
* Converts a JSON workflow configuration to a workflow configuration object.
*
* @param json JSON for workflow rule target
* @return a workflow rule target object
* @throws IOException if unable to create object
*/
public static WorkflowRuleTarget fromJson(String json) throws IOException{
ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, WorkflowRuleTarget.class);
} | /src/main/java/com/twilio/taskrouter/WorkflowRuleTarget.java |
robustness-copilot_data_754 | /**
* Find out if the Process object is already stored in the repository. It uses the fully qualified name to retrieve the entity
*
* @param userId the name of the calling user
* @param qualifiedName the qualifiedName name of the process to be searched
*
* @return optional with entity details if found, empty optional if not found
*
* @throws InvalidParameterException the bean properties are invalid
* @throws UserNotAuthorizedException user not authorized to issue this request
* @throws PropertyServerException problem accessing the property server
*/
public Optional<EntityDetail> findProcessEntity(String userId, String qualifiedName) throws UserNotAuthorizedException, PropertyServerException, InvalidParameterException{
return dataEngineCommonHandler.findEntity(userId, qualifiedName, PROCESS_TYPE_NAME);
} | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineProcessHandler.java |
robustness-copilot_data_755 | /**
* Add a custom encoder to the hash generator which will be built. Although
* not enforced, the encoder should be stateless and should not modify any
* passed inputs.
*
* @param encoder an atom encoder
* @return fluent API reference (self)
* @throws NullPointerException no encoder provided
*/
public HashGeneratorMaker encode(AtomEncoder encoder){
if (encoder == null)
throw new NullPointerException("no encoder provided");
customEncoders.add(encoder);
return this;
} | /tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java |
robustness-copilot_data_756 | /**
* Load a list of SMARTS patterns from the specified file.
*
* Each line in the file corresponds to a pattern with the following structure:
* PATTERN_DESCRIPTION: SMARTS_PATTERN, <i>e.g., Thioketone: [#6][CX3](=[SX1])[#6]</i>
*
* Empty lines and lines starting with a "#" are skipped.
*
* @param filename list of the SMARTS pattern to be loaded
* @return list of strings containing the loaded SMARTS pattern
* @throws Exception if there is an error parsing SMILES patterns
*/
private static String[] readSMARTSPattern(String filename) throws Exception{
InputStream ins = StandardSubstructureSets.class.getClassLoader().getResourceAsStream(filename);
BufferedReader reader = new BufferedReader(new InputStreamReader(ins));
List<String> tmp = new ArrayList<String>();
String line;
while ((line = reader.readLine()) != null) {
if (line.startsWith("#") || line.trim().length() == 0)
continue;
String[] toks = line.split(":");
StringBuffer s = new StringBuffer();
for (int i = 1; i < toks.length - 1; i++) s.append(toks[i] + ":");
s.append(toks[toks.length - 1]);
tmp.add(s.toString().trim());
}
return tmp.toArray(new String[] {});
} | /descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/StandardSubstructureSets.java |
robustness-copilot_data_757 | /**
* Choose a random plan from the person and return it.
* @return The newly selected plan for this person; <code>null</code> if the person has no plans.
*/
public T selectPlan(final HasPlansAndId<T, I> person){
// this used to use person.getRandomPlan(), but I inlined the function here in order to get rid of the function of the data class.
// kai, nov'13
if (person.getPlans().size() == 0) {
return null;
}
int index = (int) (MatsimRandom.getRandom().nextDouble() * person.getPlans().size());
// yyyy As far as I can tell, this produces race conditions when running multi-threaded. I.e. when running the same
// setup twice, this function may return different results per thread or per person. kai, jun'14
return person.getPlans().get(index);
} | /matsim/src/main/java/org/matsim/core/replanning/selectors/RandomPlanSelector.java |
robustness-copilot_data_758 | /**
* Persists the Users to CSV form data to the underlying jcr:content node.
* @param request the Sling HTTP Request object
* @param response the Sling HTTP Response object
* @throws IOException
* @throws ServletException
*/
public void doPost(SlingHttpServletRequest request, SlingHttpServletResponse response) throws IOException, ServletException{
response.setContentType("application/json");
response.setCharacterEncoding("UTF-8");
final ValueMap properties = request.getResource().adaptTo(ModifiableValueMap.class);
final Parameters parameters = new Parameters(request);
properties.put(GROUP_FILTER, parameters.getGroupFilter());
properties.put(GROUPS, parameters.getGroups());
properties.put(CUSTOM_PROPERTIES, parameters.getCustomProperties());
request.getResourceResolver().commit();
} | /bundle/src/main/java/com/adobe/acs/commons/exporters/impl/users/UsersSaveServlet.java |
robustness-copilot_data_759 | /**
* Return the enum value in the language specified format
* e.g. status becomes "status"
*
* @param value enum variable name
* @param datatype data type
* @return the sanitized value for enum
*/
public String toEnumValue(String value, String datatype){
if ("number".equalsIgnoreCase(datatype) || "boolean".equalsIgnoreCase(datatype)) {
return value;
} else {
return "\"" + escapeText(value) + "\"";
}
} | /modules/openapi-generator/src/main/java/org/openapitools/codegen/DefaultCodegen.java |
robustness-copilot_data_760 | /**
* Overridable factory method called by {@link #writeValues(OutputStream)}
* method (and its various overrides), and initializes it as necessary.
*
* @since 2.5
*/
protected SequenceWriter _newSequenceWriter(boolean wrapInArray, JsonGenerator gen, boolean managedInput) throws IOException{
return new SequenceWriter(_serializerProvider(), _configureGenerator(gen), managedInput, _prefetch).init(wrapInArray);
} | /src/main/java/com/fasterxml/jackson/databind/ObjectWriter.java |
robustness-copilot_data_761 | /**
* Given the current configuration create an {@link AtomHashGenerator}.
*
* @return instance of the generator
* @throws IllegalArgumentException no depth or encoders were configured
*/
public AtomHashGenerator atomic(){
if (depth < 0)
throw new IllegalArgumentException("no depth specified, use .depth(int)");
List<AtomEncoder> encoders = new ArrayList<AtomEncoder>();
for (AtomEncoder encoder : encoderSet) {
encoders.add(encoder);
}
encoders.addAll(this.customEncoders);
boolean suppress = suppression != AtomSuppression.unsuppressed();
AtomEncoder encoder = new ConjugatedAtomEncoder(encoders);
SeedGenerator seeds = new SeedGenerator(encoder, suppression);
AbstractAtomHashGenerator simple = suppress ? new SuppressedAtomHashGenerator(seeds, new Xorshift(), makeStereoEncoderFactory(), suppression, depth) : new BasicAtomHashGenerator(seeds, new Xorshift(), makeStereoEncoderFactory(), depth);
if (equivSetFinder != null) {
return new PerturbedAtomHashGenerator(seeds, simple, new Xorshift(), makeStereoEncoderFactory(), equivSetFinder, suppression);
} else {
return simple;
}
} | /tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java |
robustness-copilot_data_762 | /**
* Normalises a 5-member 'cycle' such that the hetroatom contributing the lone-pair is in
* position 1 (index 0). The alpha atoms are then in index 1 and 4 whilst the beta atoms are in
* index 2 and 3. If the ring contains more than one hetroatom the cycle is not normalised
* (return=false).
*
* @param cycle aromatic cycle to normalise, |C| = 5
* @param contribution vector of p electron contributions from each vertex (size |V|)
* @return whether the cycle was normalised
*/
static boolean normaliseCycle(int[] cycle, int[] contribution){
int offset = indexOfHetro(cycle, contribution);
if (offset < 0)
return false;
if (offset == 0)
return true;
int[] cpy = Arrays.copyOf(cycle, cycle.length);
int len = cycle.length - 1;
for (int j = 0; j < len; j++) {
cycle[j] = cpy[(offset + j) % len];
}
cycle[len] = cycle[0];
return true;
} | /tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java |
robustness-copilot_data_763 | /**
* Will return the name of the last folder in pathName. Takes root folder into account.
* When called with argument "/folder", return value is "folder".
* When called with argument "/", return value is "/"
*
* @param pathName path
*
* @return folder name
*/
private String computeDisplayName(String pathName){
return new File(pathName).getName().length() < 1 ? pathName : new File(pathName).getName();
} | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineFolderHierarchyHandler.java |
robustness-copilot_data_764 | /**
* Combines the values in an n x m matrix into a single array of size n.
* This process scans the rows and xors all unique values in the row
* together. If a duplicate value is found it is rotated using a
* pseudorandom number generator.
*
* @param perturbed n x m, matrix
* @return the combined values of each row
*/
long[] combine(long[][] perturbed){
int n = perturbed.length;
int m = perturbed[0].length;
long[] combined = new long[n];
long[] rotated = new long[m];
for (int i = 0; i < n; i++) {
Arrays.sort(perturbed[i]);
for (int j = 0; j < m; j++) {
if (j > 0 && perturbed[i][j] == perturbed[i][j - 1]) {
combined[i] ^= rotated[j] = rotate(rotated[j - 1]);
} else {
combined[i] ^= rotated[j] = perturbed[i][j];
}
}
}
return combined;
} | /tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java |
robustness-copilot_data_765 | /**
* Ensure that a Checksum is calculated for the supplied ChecksumType. If the ChecksumType is
* already registered then this method does nothing, otherwise the ChecksumChannel is updated to
* calculate the new ChecksumType. If the ChecksumChannel has accepted a contiguous range of
* data from offset 0 then this method will reread that contiguous range.
*
* @param type The algorithm this ChecksumChannel should calculate.
* @throws IOException if the Channel has already started accepting data and an attempt to
* reread data from disk fails.
*/
public void addType(ChecksumType type) throws IOException{
synchronized (_digests) {
if (_digests.stream().map(MessageDigest::getAlgorithm).noneMatch(t -> t.equals(type.getName()))) {
MessageDigest digest = type.createMessageDigest();
if (_isChecksumViable) {
try {
updateFromChannel(Collections.singleton(digest), 0L, _nextChecksumOffset);
} catch (IOException e) {
throw new IOException("Failed when reading received data: " + messageOrClassName(e), e);
}
}
_digests.add(digest);
}
}
} | /modules/dcache/src/main/java/org/dcache/pool/movers/ChecksumChannel.java |
robustness-copilot_data_766 | /**
* Method that will set value of specified property if (and only if)
* it had no set value previously.
* Note that explicitly set {@code null} is a value.
* Functionally equivalent to:
*<code>
* if (get(propertyName) == null) {
* set(propertyName, value);
* return null;
* } else {
* return get(propertyName);
* }
*</code>
*
* @param propertyName Name of property to set
* @param value Value to set to property (if and only if it had no value previously);
* if null, will be converted to a {@link NullNode} first.
*
* @return Old value of the property, if any (in which case value was not changed);
* null if there was no old value (in which case value is now set)
*
* @since 2.13
*/
public JsonNode putIfAbsent(String propertyName, JsonNode value){
if (value == null) {
value = nullNode();
}
return _children.putIfAbsent(propertyName, value);
} | /src/main/java/com/fasterxml/jackson/databind/node/ObjectNode.java |
robustness-copilot_data_767 | /**
* Pop frame off front of message, caller now owns frame.
* If next frame is empty, pops and destroys that empty frame
* (e.g. useful when unwrapping ROUTER socket envelopes)
* @return
* Unwrapped frame
*/
public ZFrame unwrap(){
if (size() == 0) {
return null;
}
ZFrame f = pop();
ZFrame empty = getFirst();
if (empty.hasData() && empty.size() == 0) {
empty = pop();
empty.destroy();
}
return f;
} | /src/main/java/org/zeromq/ZMsg.java |
robustness-copilot_data_768 | /**
* Appends a throwable and recursively appends its causedby/suppressed throwables
* in "normal" order (Root cause last).
*/
private void appendRootCauseLast(StringBuilder builder, String prefix, int indent, IThrowableProxy throwableProxy, Deque<String> stackHashes){
if (throwableProxy == null || builder.length() > maxLength) {
return;
}
String hash = stackHashes == null || stackHashes.isEmpty() ? null : stackHashes.removeFirst();
appendFirstLine(builder, prefix, indent, throwableProxy, hash);
appendStackTraceElements(builder, indent, throwableProxy);
IThrowableProxy[] suppressedThrowableProxies = throwableProxy.getSuppressed();
if (suppressedThrowableProxies != null) {
for (IThrowableProxy suppressedThrowableProxy : suppressedThrowableProxies) {
appendRootCauseLast(builder, CoreConstants.SUPPRESSED, indent + ThrowableProxyUtil.SUPPRESSED_EXCEPTION_INDENT, suppressedThrowableProxy, null);
}
}
appendRootCauseLast(builder, CoreConstants.CAUSED_BY, indent, throwableProxy.getCause(), stackHashes);
} | /src/main/java/net/logstash/logback/stacktrace/ShortenedThrowableConverter.java |
robustness-copilot_data_769 | /**
* Locates by query all the ACLs that the principal participates in.
*
* @param resourceResolver the resource resolver to perform the user management
* @param principalName the principal name
* @param accessControlManager Jackrabbit access control manager
* @return a list of ACLs that principal participates in.
*/
private List<JackrabbitAccessControlList> findAcls(ResourceResolver resourceResolver, String principalName, JackrabbitAccessControlManager accessControlManager){
final Set<String> paths = new HashSet<String>();
final List<JackrabbitAccessControlList> acls = new ArrayList<JackrabbitAccessControlList>();
final Map<String, String> params = new HashMap<String, String>();
params.put("type", PROP_NT_REP_ACE);
params.put("property", PROP_REP_PRINCIPAL_NAME);
params.put("property.value", principalName);
params.put("p.limit", "-1");
Query query = queryBuilder.createQuery(PredicateGroup.create(params), resourceResolver.adaptTo(Session.class));
QueryUtil.setResourceResolverOn(resourceResolver, query);
for (final Hit hit : query.getResult().getHits()) {
try {
final Resource aceResource = resourceResolver.getResource(hit.getPath());
final Resource contentResource = aceResource.getParent().getParent();
if (!paths.contains(contentResource.getPath())) {
paths.add(contentResource.getPath());
for (AccessControlPolicy policy : accessControlManager.getPolicies(contentResource.getPath())) {
if (policy instanceof JackrabbitAccessControlList) {
acls.add((JackrabbitAccessControlList) policy);
break;
}
}
}
} catch (RepositoryException e) {
log.error("Failed to get resource for query result.", e);
}
}
return acls;
} | /bundle/src/main/java/com/adobe/acs/commons/users/impl/EnsureAce.java |
robustness-copilot_data_770 | /**
* Special case, 'NCN+' matches entries that the validation suite say should actually be 'NC=N'.
* We can achieve 100% compliance by checking if NCN+ is still next to CNN+ or CIM+ after
* aromatic types are assigned
*
* @param symbs symbolic types
* @param graph adjacency list graph
*/
private void fixNCNTypes(String[] symbs, int[][] graph){
for (int v = 0; v < graph.length; v++) {
if ("NCN+".equals(symbs[v])) {
boolean foundCNN = false;
for (int w : graph[v]) {
foundCNN = foundCNN || "CNN+".equals(symbs[w]) || "CIM+".equals(symbs[w]);
}
if (!foundCNN) {
symbs[v] = "NC=N";
}
}
}
} | /tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAtomTypeMatcher.java |
robustness-copilot_data_771 | /**
* Test if set sourceBitSet is contained in set targetBitSet.
* @param sourceBitSet a bitSet
* @param targetBitSet a bitSet
* @return true if sourceBitSet is contained in targetBitSet
*/
private boolean isContainedIn(BitSet sourceBitSet, BitSet targetBitSet){
boolean result = false;
if (sourceBitSet.isEmpty()) {
return true;
}
BitSet setA = (BitSet) sourceBitSet.clone();
setA.and(targetBitSet);
if (setA.equals(sourceBitSet)) {
result = true;
}
return result;
} | /legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRGraph.java |
robustness-copilot_data_772 | /**
* Takes the passed info object and updated the internal fields according to it.
* @param inf the info from which we update the fields.
*/
public void applyDisplayInfo(AuthenticatedUserDisplayInfo inf){
setFirstName(inf.getFirstName());
setLastName(inf.getLastName());
if (nonEmpty(inf.getEmailAddress())) {
setEmail(inf.getEmailAddress());
}
if (nonEmpty(inf.getAffiliation())) {
setAffiliation(inf.getAffiliation());
}
if (nonEmpty(inf.getPosition())) {
setPosition(inf.getPosition());
}
} | /src/main/java/edu/harvard/iq/dataverse/authorization/users/AuthenticatedUser.java |
robustness-copilot_data_773 | /**
* Method called to ensure that given parser is ready for reading
* content for data binding.
*
* @return First token to be used for data binding after this call:
* can never be null as exception will be thrown if parser cannot
* provide more tokens.
*
* @throws IOException if the underlying input source has problems during
* parsing
*/
protected JsonToken _initForReading(JsonParser p, JavaType targetType) throws IOException{
_deserializationConfig.initialize(p);
JsonToken t = p.currentToken();
if (t == null) {
t = p.nextToken();
if (t == null) {
throw MismatchedInputException.from(p, targetType, "No content to map due to end-of-input");
}
}
return t;
} | /src/main/java/com/fasterxml/jackson/databind/ObjectMapper.java |
robustness-copilot_data_774 | /**
* Adds a change listener to the list of listeners.
*
* @param listener
* The listener added to the list
*/
public void addCDKChangeListener(ICDKChangeListener listener){
if (listeners == null) {
listeners = new ArrayList<ICDKChangeListener>();
}
if (!listeners.contains(listener)) {
listeners.add(listener);
}
} | /display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java |
robustness-copilot_data_775 | /**
* Execute the task while the Thread Context Class Loader is set to the provided
* Class Loader.
*
* @param classLoader the requested class loader
* @param task the task
* @param <V> the return type of the task
* @return the return value
* @throws Exception the exception throw, if any, by the task
*/
public static V doWithTccl(ClassLoader classLoader, Callable<V> task) throws Exception{
ClassLoader oldClassLoader = Thread.currentThread().getContextClassLoader();
Thread.currentThread().setContextClassLoader(classLoader);
try {
return task.call();
} finally {
Thread.currentThread().setContextClassLoader(oldClassLoader);
}
} | /bundle/src/main/java/com/adobe/acs/commons/util/ThreadContextClassLoaderTaskExecutor.java |
robustness-copilot_data_776 | /**
* Adds patches to the specified patch builder to correct differences in the current vs required
* maps.
*
* @param patchBuilder a builder for the patches
* @param basePath the base for the patch path (excluding the name)
* @param current a map of the values found in a Kubernetes resource
* @param required a map of the values specified for the resource by the domain
*/
static void addPatches(JsonPatchBuilder patchBuilder, String basePath, Map<String, String> current, Map<String, String> required){
for (String name : required.keySet()) {
String encodedPath = basePath + name.replace("~", "~0").replace("/", "~1");
if (!current.containsKey(name)) {
patchBuilder.add(encodedPath, required.get(name));
} else {
patchBuilder.replace(encodedPath, required.get(name));
}
}
} | /operator/src/main/java/oracle/kubernetes/operator/helpers/KubernetesUtils.java |
robustness-copilot_data_777 | /**
* Splits this partition by taking the cell at cellIndex and making two
* new cells - the first with the the rest of the elements from that cell
* and the second with the singleton splitElement.
*
* @param cellIndex the index of the cell to split on
* @param splitElement the element to put in its own cell
* @return a new (finer) Partition
*/
public Partition splitAfter(int cellIndex, int splitElement){
Partition r = new Partition();
for (int j = 0; j < cellIndex; j++) {
r.addCell(this.copyBlock(j));
}
SortedSet<Integer> splitBlock = this.copyBlock(cellIndex);
splitBlock.remove(splitElement);
r.addCell(splitBlock);
r.addSingletonCell(splitElement);
for (int j = cellIndex + 1; j < this.size(); j++) {
r.addCell(this.copyBlock(j));
}
return r;
} | /tool/group/src/main/java/org/openscience/cdk/group/Partition.java |
robustness-copilot_data_778 | /**
* Finds a neighbor attached to 'atom' that is singley bonded and isn't
* 'exclude'. If no such atom exists, the 'atom' is returned.
*
* @param container a molecule container
* @param atom the atom to find the neighbor or
* @param exclude don't find this atom
* @return the other atom (or 'atom')
*/
private static IAtom findOtherSinglyBonded(IAtomContainer container, IAtom atom, IAtom exclude){
for (final IBond bond : container.getConnectedBondsList(atom)) {
if (!IBond.Order.SINGLE.equals(bond.getOrder()) || bond.contains(exclude))
continue;
return bond.getOther(atom);
}
return atom;
} | /storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java |
robustness-copilot_data_779 | /**
* Creates a new discretizer with bin borders defined such that each bin
* would contain approximately <tt>size</tt> samples from <tt>samples</tt>.
*
* Samples are sorted into bins in ascending order. If there are not
* sufficient (less than <tt>size</tt>) samples to fill a further bin, the
* remaining samples are sorted into the last bin. That is, the last bin is
* the only bin that may contain more than <tt>size</tt> samples.
*
* @param samples
* an array with samples.
* @param size
* the number of samples per bin.
* @return a new discretizer.
*/
public static FixedBordersDiscretizer create(double[] samples, int size){
TDoubleArrayList borders;
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
TDoubleIntHashMap hist = new TDoubleIntHashMap(samples.length);
for (int i = 0; i < samples.length; i++) {
hist.adjustOrPutValue(samples[i], 1, 1);
min = Math.min(min, samples[i]);
max = Math.max(max, samples[i]);
}
double[] keys = hist.keys();
Arrays.sort(keys);
borders = new TDoubleArrayList(keys.length);
borders.add(min - 1E-10);
int binsize = 0;
int n = 0;
for (int i = 0; i < keys.length; i++) {
int nBin = hist.get(keys[i]);
binsize += nBin;
n += nBin;
if (binsize >= size && i > 0) {
// sufficient samples for the
// current bin
if (samples.length - n >= binsize) {
// sufficient remaining
// samples to fill the
// next bin
borders.add(keys[i]);
binsize = 0;
}
}
}
if (binsize > 0)
borders.add(max);
return new FixedBordersDiscretizer(borders.toArray());
} | /contribs/common/src/main/java/org/matsim/contrib/common/stats/FixedSampleSizeDiscretizer.java |
robustness-copilot_data_780 | /**
* Reads partial atomic charges and add the to the given ChemModel.
*
* @param model Description of the Parameter
* @throws CDKException Description of the Exception
* @throws IOException Description of the Exception
*/
private void readPartialCharges(IChemModel model) throws CDKException, IOException{
logger.info("Reading partial atomic charges");
IAtomContainerSet moleculeSet = model.getMoleculeSet();
IAtomContainer molecule = moleculeSet.getAtomContainer(0);
String line = input.readLine();
while (input.ready()) {
line = input.readLine();
logger.debug("Read charge block line: " + line);
if ((line == null) || (line.indexOf("Sum of Mulliken charges") >= 0)) {
logger.debug("End of charge block found");
break;
}
StringReader sr = new StringReader(line);
StreamTokenizer tokenizer = new StreamTokenizer(sr);
if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
int atomCounter = (int) tokenizer.nval;
tokenizer.nextToken();
double charge;
if (tokenizer.nextToken() == StreamTokenizer.TT_NUMBER) {
charge = tokenizer.nval;
logger.debug("Found charge for atom " + atomCounter + ": " + charge);
} else {
throw new CDKException("Error while reading charge: expected double.");
}
IAtom atom = molecule.getAtom(atomCounter - 1);
atom.setCharge(charge);
}
}
} | /storage/io/src/main/java/org/openscience/cdk/io/Gaussian98Reader.java |
robustness-copilot_data_781 | /**
* Reorders the {@link ILigand} objects in the array according to the CIP rules.
*
* @param ligands Array of {@link ILigand}s to be reordered.
* @return Reordered array of {@link ILigand}s.
*/
public static ILigand[] order(ILigand[] ligands){
ILigand[] newLigands = new ILigand[ligands.length];
System.arraycopy(ligands, 0, newLigands, 0, ligands.length);
Arrays.sort(newLigands, cipRule);
return newLigands;
} | /descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java |
robustness-copilot_data_782 | /**
* Connect and initialize a channel from {@link ConnectionBuilder}.
*
* @param connectionBuilder must not be {@code null}.
* @return the {@link ConnectionFuture} to synchronize the connection process.
* @since 4.4
*/
protected ConnectionFuture<T> initializeChannelAsync(ConnectionBuilder connectionBuilder){
Mono<SocketAddress> socketAddressSupplier = connectionBuilder.socketAddress();
if (clientResources.eventExecutorGroup().isShuttingDown()) {
throw new IllegalStateException("Cannot connect, Event executor group is terminated.");
}
CompletableFuture<SocketAddress> socketAddressFuture = new CompletableFuture<>();
CompletableFuture<Channel> channelReadyFuture = new CompletableFuture<>();
socketAddressSupplier.doOnError(socketAddressFuture::completeExceptionally).doOnNext(socketAddressFuture::complete).subscribe(redisAddress -> {
if (channelReadyFuture.isCancelled()) {
return;
}
initializeChannelAsync0(connectionBuilder, channelReadyFuture, redisAddress);
}, channelReadyFuture::completeExceptionally);
return new DefaultConnectionFuture<>(socketAddressFuture, channelReadyFuture.thenApply(channel -> (T) connectionBuilder.connection()));
} | /src/main/java/io/lettuce/core/AbstractRedisClient.java |
robustness-copilot_data_783 | /**
* Tries double bond combinations for a certain input container of which the double bonds have been stripped
* around the mobile hydrogen positions. Recursively.
*
* @param container
* @param dblBondsAdded counts double bonds added so far
* @param bondOffSet offset for next double bond position to consider
* @param doubleBondMax maximum number of double bonds to add
* @param atomsInNeedOfFix atoms that require more bonds
* @return a list of double bond positions (index) that make a valid combination, null if none found
*/
private List<Integer> tryDoubleBondCombinations(IAtomContainer container, int dblBondsAdded, int bondOffSet, int doubleBondMax, List<IAtom> atomsInNeedOfFix){
int offSet = bondOffSet;
List<Integer> dblBondPositions = null;
while (offSet < container.getBondCount() && dblBondPositions == null) {
IBond bond = container.getBond(offSet);
if (atomsInNeedOfFix.contains(bond.getBegin()) && atomsInNeedOfFix.contains(bond.getEnd())) {
bond.setOrder(IBond.Order.DOUBLE);
dblBondsAdded = dblBondsAdded + 1;
if (dblBondsAdded == doubleBondMax) {
boolean validDoubleBondConfig = true;
CHECK: for (IAtom atom : container.atoms()) {
if (atom.getValency() != atom.getImplicitHydrogenCount() + getConnectivity(atom, container)) {
validDoubleBondConfig = false;
break CHECK;
}
}
if (validDoubleBondConfig) {
dblBondPositions = new ArrayList<Integer>();
for (int idx = 0; idx < container.getBondCount(); idx++) {
if (container.getBond(idx).getOrder().equals(IBond.Order.DOUBLE))
dblBondPositions.add(idx);
}
return dblBondPositions;
}
} else {
dblBondPositions = tryDoubleBondCombinations(container, dblBondsAdded, offSet + 1, doubleBondMax, atomsInNeedOfFix);
}
bond.setOrder(IBond.Order.SINGLE);
dblBondsAdded = dblBondsAdded - 1;
}
offSet++;
}
return dblBondPositions;
} | /tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java |
robustness-copilot_data_784 | /**
* Extract the charge position given a molecular formula format [O3S]2-.
*
* @param formula The formula to inspect
* @return The charge position in the string
*/
private static int findChargePosition(String formula){
int end = formula.length() - 1;
int pos = end;
while (pos >= 0 && isSign(formula.charAt(pos))) pos--;
int mark1 = pos;
while (pos >= 0 && isDigit(formula.charAt(pos))) pos--;
int mark2 = pos;
while (pos >= 0 && isSign(formula.charAt(pos))) pos--;
if (pos == mark2 && formula.charAt(pos) != ']')
pos = mark1;
return pos + 1;
} | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_785 | /**
* Judge whether current sharding items are all register start success.
*
* @param shardingItems current sharding items
* @return current sharding items are all start success or not
*/
public boolean isRegisterStartSuccess(final Collection<Integer> shardingItems){
for (int each : shardingItems) {
if (!jobNodeStorage.isJobNodeExisted(GuaranteeNode.getStartedNode(each))) {
return false;
}
}
return true;
} | /elasticjob-lite/elasticjob-lite-core/src/main/java/org/apache/shardingsphere/elasticjob/lite/internal/guarantee/GuaranteeService.java |
robustness-copilot_data_786 | /**
* Obtain the parity (winding) of a tetrahedral element. The parity is -1
* for clockwise (odd), +1 for anticlockwise (even) and 0 for unspecified.
*
* @param stereo configuration
* @return the parity
*/
private int parity(ITetrahedralChirality.Stereo stereo){
switch(stereo) {
case CLOCKWISE:
return -1;
case ANTI_CLOCKWISE:
return +1;
default:
return 0;
}
} | /tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java |
robustness-copilot_data_787 | /**
* Main method which assigns Gasteiger Marisili partial sigma charges.
*
*@param ac AtomContainer
*@param setCharge The Charge
*@return AtomContainer with partial charges
*@exception Exception Possible Exceptions
*/
public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge) throws Exception{
for (int i = 0; i < ac.getAtomCount(); i++) ac.getAtom(i).setCharge(0.0);
double[] gasteigerFactors = assignGasteigerSigmaMarsiliFactors(ac);
double alpha = 1.0;
double q;
double deoc;
IAtom[] atoms = null;
int atom1 = 0;
int atom2 = 0;
double[] q_old = new double[ac.getAtomCount()];
for (int i = 0; i < q_old.length; i++) q_old[0] = 20.0;
out: for (int i = 0; i < MX_ITERATIONS; i++) {
alpha *= MX_DAMP;
boolean isDifferent = false;
for (int j = 0; j < ac.getAtomCount(); j++) {
q = gasteigerFactors[STEP_SIZE * j + j + 5];
double difference = Math.abs(q_old[j]) - Math.abs(q);
if (Math.abs(difference) > 0.001)
isDifferent = true;
q_old[j] = q;
gasteigerFactors[STEP_SIZE * j + j + 4] = gasteigerFactors[STEP_SIZE * j + j + 2] * q * q + gasteigerFactors[STEP_SIZE * j + j + 1] * q + gasteigerFactors[STEP_SIZE * j + j];
}
if (!isDifferent)
break out;
Iterator<IBond> bonds = ac.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
atom1 = ac.indexOf(bond.getBegin());
atom2 = ac.indexOf(bond.getEnd());
if (gasteigerFactors[STEP_SIZE * atom1 + atom1 + 4] >= gasteigerFactors[STEP_SIZE * atom2 + atom2 + 4]) {
if ("H".equals(ac.getAtom(atom2).getSymbol())) {
deoc = DEOC_HYDROGEN;
} else {
deoc = gasteigerFactors[STEP_SIZE * atom2 + atom2 + 3];
}
} else {
if ("H".equals(ac.getAtom(atom1).getSymbol())) {
deoc = DEOC_HYDROGEN;
} else {
deoc = gasteigerFactors[STEP_SIZE * atom1 + atom1 + 3];
}
}
q = (gasteigerFactors[STEP_SIZE * atom1 + atom1 + 4] - gasteigerFactors[STEP_SIZE * atom2 + atom2 + 4]) / deoc;
gasteigerFactors[STEP_SIZE * atom1 + atom1 + 5] -= (q * alpha);
gasteigerFactors[STEP_SIZE * atom2 + atom2 + 5] += (q * alpha);
}
}
for (int i = 0; i < ac.getAtomCount(); i++) {
ac.getAtom(i).setCharge(gasteigerFactors[STEP_SIZE * i + i + 5]);
}
return ac;
} | /tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java |
robustness-copilot_data_788 | /**
* Performs a breadthFirstSearch in an AtomContainer starting with a
* particular sphere, which usually consists of one start atom, and searches
* for the longest aliphatic chain which is yet unplaced. If the search
* encounters an unplaced ring atom, it is also appended to the chain so that
* this last bond of the chain can also be laid out. This gives us the
* orientation for the attachment of the ring system.
*
*@param ac The AtomContainer to
* be searched
*@param sphere A sphere of atoms to
* start the search with
*@param pathes A vector of N pathes
* (N = no of heavy atoms).
*@exception org.openscience.cdk.exception.CDKException Description of the
* Exception
*/
public static void breadthFirstSearch(IAtomContainer ac, List<IAtom> sphere, IAtomContainer[] pathes) throws CDKException{
IAtom atom = null;
IAtom nextAtom = null;
int atomNr;
int nextAtomNr;
List<IAtom> newSphere = new ArrayList<IAtom>();
logger.debug("Start of breadthFirstSearch");
for (int f = 0; f < sphere.size(); f++) {
atom = sphere.get(f);
if (!atom.getFlag(CDKConstants.ISINRING)) {
atomNr = ac.indexOf(atom);
logger.debug("BreadthFirstSearch around atom " + (atomNr + 1));
List bonds = ac.getConnectedBondsList(atom);
for (int g = 0; g < bonds.size(); g++) {
IBond curBond = (IBond) bonds.get(g);
nextAtom = curBond.getOther(atom);
if (!nextAtom.getFlag(CDKConstants.VISITED) && !nextAtom.getFlag(CDKConstants.ISPLACED)) {
nextAtomNr = ac.indexOf(nextAtom);
logger.debug("BreadthFirstSearch is meeting new atom " + (nextAtomNr + 1));
pathes[nextAtomNr] = ac.getBuilder().newInstance(IAtomContainer.class, pathes[atomNr]);
logger.debug("Making copy of path " + (atomNr + 1) + " to form new path " + (nextAtomNr + 1));
pathes[nextAtomNr].addAtom(nextAtom);
logger.debug("Adding atom " + (nextAtomNr + 1) + " to path " + (nextAtomNr + 1));
pathes[nextAtomNr].addBond(curBond);
if (ac.getConnectedBondsCount(nextAtom) > 1) {
newSphere.add(nextAtom);
}
}
}
}
}
if (newSphere.size() > 0) {
for (int f = 0; f < newSphere.size(); f++) {
newSphere.get(f).setFlag(CDKConstants.VISITED, true);
}
breadthFirstSearch(ac, newSphere, pathes);
}
logger.debug("End of breadthFirstSearch");
} | /tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java |
robustness-copilot_data_789 | /**
* Exclude subsequent generated nodes, if they are consecutive and on the same line.
*/
private static boolean isGeneratedNodeExcluded(AstNode astNode){
var prev = astNode.getPreviousAstNode();
return prev != null && prev.getTokenLine() == astNode.getTokenLine() && prev.isCopyBookOrGeneratedNode();
} | /cxx-checks/src/main/java/org/sonar/cxx/checks/metrics/TooManyStatementsPerLineCheck.java |
robustness-copilot_data_790 | /**
* Creates a new module / config-group with the specified name.
*
* @param name
* The name of the config-group to be created.
*
* @return the newly created config group
* @throws IllegalArgumentException
* if a config-group with the specified name already exists.
*/
public final ConfigGroup createModule(final String name){
if (this.modules.containsKey(name)) {
throw new IllegalArgumentException("Module " + name + " exists already.");
}
ConfigGroup m = new ConfigGroup(name);
this.modules.put(name, m);
return m;
} | /matsim/src/main/java/org/matsim/core/config/Config.java |
robustness-copilot_data_791 | /**
* Method called to locate deserializer ahead of time, if permitted
* by configuration. Method also is NOT to throw an exception if
* access fails.
*/
protected JsonDeserializer<Object> _prefetchRootDeserializer(JavaType valueType){
if ((valueType == null) || !_config.isEnabled(DeserializationFeature.EAGER_DESERIALIZER_FETCH)) {
return null;
}
JsonDeserializer<Object> deser = _rootDeserializers.get(valueType);
if (deser == null) {
try {
DeserializationContext ctxt = createDummyDeserializationContext();
deser = ctxt.findRootValueDeserializer(valueType);
if (deser != null) {
_rootDeserializers.put(valueType, deser);
}
return deser;
} catch (JacksonException e) {
}
}
return deser;
} | /src/main/java/com/fasterxml/jackson/databind/ObjectReader.java |
robustness-copilot_data_792 | /**
* Generate a new geometric parity (2D or 3D) for the given molecule and
* atom indices. This method ensure that 2D and 3D coordinates are available
* on the specified atoms and returns null if the 2D or 3D coordinates are
* not fully available.
*
* @param mol a molecule
* @param l left double bonded atom
* @param r right double bonded atom
* @param l1 first substituent atom of <i>l</i>
* @param l2 second substituent atom of <i>l</i> or <i>l</i> if there is
* none
* @param r1 first substituent atom of <i>r</i>
* @param r2 second substituent atom of <i>r</i> or <i>r</i> if there is
* none
* @return geometric parity or null
*/
static GeometricParity geometric(IAtomContainer mol, int l, int r, int l1, int l2, int r1, int r2){
Point2d l2d = mol.getAtom(l).getPoint2d();
Point2d r2d = mol.getAtom(r).getPoint2d();
Point2d l12d = mol.getAtom(l1).getPoint2d();
Point2d l22d = mol.getAtom(l2).getPoint2d();
Point2d r12d = mol.getAtom(r1).getPoint2d();
Point2d r22d = mol.getAtom(r2).getPoint2d();
if (l2d != null && r2d != null && l12d != null && l22d != null && r12d != null && r22d != null) {
return new DoubleBond2DParity(l2d, r2d, l12d, l22d, r12d, r22d);
}
Point3d l3d = mol.getAtom(l).getPoint3d();
Point3d r3d = mol.getAtom(r).getPoint3d();
Point3d l13d = mol.getAtom(l1).getPoint3d();
Point3d r13d = mol.getAtom(r1).getPoint3d();
if (l3d != null && r3d != null && l13d != null && r13d != null)
return new DoubleBond3DParity(l3d, r3d, l13d, r13d);
return null;
} | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java |
robustness-copilot_data_793 | /**
* Given a file path, loads the contents of the files into a map.
*
* @param rootDir the path to the top-level directory
* @return a map of file names to string contents.
* @throws IOException if an error occurs during the read
*/
static Map<String, String> loadContents(Path rootDir) throws IOException{
try (Stream<Path> walk = Files.walk(rootDir, 1)) {
return walk.filter(path -> !Files.isDirectory(path)).collect(Collectors.toMap(FileGroupReader::asString, FileGroupReader::readContents));
}
} | /operator/src/main/java/oracle/kubernetes/operator/helpers/FileGroupReader.java |
robustness-copilot_data_794 | /**
* Find out if the entity is already stored in the repository. It uses the fully qualified name to retrieve the entity
*
* @param userId the name of the calling user
* @param qualifiedName the qualifiedName name of the entity to be searched
* @param entityTypeName the type name of the entity
*
* @return optional with entity details if found, empty optional if not found
*
* @throws InvalidParameterException the bean properties are invalid
* @throws UserNotAuthorizedException user not authorized to issue this request
* @throws PropertyServerException problem accessing the property server
*/
public Optional<EntityDetail> findEntity(String userId, String qualifiedName, String entityTypeName) throws UserNotAuthorizedException, PropertyServerException, InvalidParameterException{
final String methodName = "findEntity";
invalidParameterHandler.validateUserId(userId, methodName);
invalidParameterHandler.validateName(qualifiedName, CommonMapper.QUALIFIED_NAME_PROPERTY_NAME, methodName);
qualifiedName = repositoryHelper.getExactMatchRegex(qualifiedName);
InstanceProperties properties = repositoryHelper.addStringPropertyToInstance(serviceName, null, CommonMapper.QUALIFIED_NAME_PROPERTY_NAME, qualifiedName, methodName);
TypeDef entityTypeDef = repositoryHelper.getTypeDefByName(userId, entityTypeName);
Optional<EntityDetail> retrievedEntity = Optional.ofNullable(repositoryHandler.getUniqueEntityByName(userId, qualifiedName, CommonMapper.QUALIFIED_NAME_PROPERTY_NAME, properties, entityTypeDef.getGUID(), entityTypeDef.getName(), methodName));
log.trace("Searching for entity with qualifiedName: {}. Result is {}", qualifiedName, retrievedEntity.map(InstanceHeader::getGUID).orElse(null));
return retrievedEntity;
} | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineCommonHandler.java |
robustness-copilot_data_795 | /**
* Atom-atom mapping of the input molecule to the bare container constructed from the InChI connection table.
* This makes it possible to map the positions of the mobile hydrogens in the InChI back to the input molecule.
* @param inchiMolGraph molecule (bare) as defined in InChI
* @param mol user input molecule
* @throws CDKException
*/
private void mapInputMoleculeToInchiMolgraph(IAtomContainer inchiMolGraph, IAtomContainer mol) throws CDKException{
Iterator<Map<IAtom, IAtom>> iter = org.openscience.cdk.isomorphism.VentoFoggia.findIdentical(inchiMolGraph, AtomMatcher.forElement(), BondMatcher.forAny()).matchAll(mol).limit(1).toAtomMap().iterator();
if (iter.hasNext()) {
for (Map.Entry<IAtom, IAtom> e : iter.next().entrySet()) {
IAtom src = e.getKey();
IAtom dst = e.getValue();
String position = src.getID();
dst.setID(position);
LOGGER.debug("Mapped InChI ", src.getSymbol(), " ", src.getID(), " to ", dst.getSymbol(), " " + dst.getID());
}
} else {
throw new IllegalArgumentException(CANSMI.create(inchiMolGraph) + " " + CANSMI.create(mol));
}
} | /tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java |
robustness-copilot_data_796 | /**
* Waits for the counter to change to a value different from
* <code>value</code>.
* <p>
* The method returns when one of the following happens:
* <p>
* * The current counter value is different from the
* <code>value</code> argument; or
* <p>
* * Some other thread invokes the <code>increment</code> method for this AtomicCounter; or
* <p>
* * Some other thread interrupts the current thread; or
* <p>
* * The specified deadline elapses; or
* <p>
* * A "spurious wakeup" occurs.
*
* @param value the value to wait for the counter to change away from
* @param deadline the absolute time to wait until
* @return true if the counter has a different value than {@code value} upon return
* @throw InterruptedException if the current thread is interrupted
*/
public boolean awaitChangeUntil(int value, Date deadline) throws InterruptedException{
_lock.lock();
try {
inLock();
return _counter != value || _updated.awaitUntil(deadline);
} finally {
_lock.unlock();
}
} | /modules/common/src/main/java/org/dcache/util/AtomicCounter.java |
robustness-copilot_data_797 | /**
* Shift the containers in a reaction vertically upwards to not overlap
* with the reference Rectangle2D. The shift is such that the given
* gap is realized, but only if the reactions are actually overlapping.
*
* @param reaction the reaction to shift
* @param bounds the bounds of the reaction to shift
* @param last the bounds of the last reaction
* @return the Rectangle2D of the shifted reaction
*/
public static Rectangle2D shiftReactionVertical(IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap){
if (last.getMaxY() + gap >= bounds.getMinY()) {
double yShift = bounds.getHeight() + last.getHeight() + gap;
Vector2d shift = new Vector2d(0, yShift);
List<IAtomContainer> containers = ReactionManipulator.getAllAtomContainers(reaction);
for (IAtomContainer container : containers) {
translate2D(container, shift);
}
return new Rectangle2D.Double(bounds.getX(), bounds.getY() + yShift, bounds.getWidth(), bounds.getHeight());
} else {
return bounds;
}
} | /legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java |
robustness-copilot_data_798 | /**
* Add a new singleton cell to the end of the partition containing only
* this element.
*
* @param element the element to add in its own cell
*/
public void addSingletonCell(int element){
SortedSet<Integer> cell = new TreeSet<Integer>();
cell.add(element);
this.cells.add(cell);
} | /tool/group/src/main/java/org/openscience/cdk/group/Partition.java |
robustness-copilot_data_799 | /**
* Convert a binary representation back into an event receiver's list of desired events.
*
* @param data the binary data
* @return a Map between the target and its set of desired event types.
* @throws IllegalArgumentException if the data is badly formatted.
*/
public static Map<PnfsId, EnumSet<EventType>> fromZkData(byte[] data){
checkArgument(data.length > 1, "Too little data");
checkArgument(data[0] == 0, "Wrong format");
Map<PnfsId, EnumSet<EventType>> deserialised = new HashMap<>();
int index = 1;
while (index < data.length) {
checkArgument(data.length - index >= 3, "Too little data for bitmask");
short bitmask = (short) (data[index++] << 8 | data[index++] & 0xFF);
EnumSet<EventType> eventTypes = Arrays.stream(EventType.values()).filter(t -> (bitmask & 1 << t.ordinal()) != 0).collect(Collectors.toCollection(() -> EnumSet.noneOf(EventType.class)));
byte length = data[index++];
checkArgument(data.length - index >= length, "Too little data for PNFSID");
PnfsId id = new PnfsId(BaseEncoding.base16().encode(data, index, length));
index += length;
deserialised.put(id, eventTypes);
LOGGER.debug("Adding id={} bitmask={} types={}", id, bitmask, eventTypes);
}
return deserialised;
} | /modules/dcache/src/main/java/diskCacheV111/namespace/EventNotifier.java |
robustness-copilot_data_800 | /**
* Exchange the elements at index i with that at index j.
*
* @param values an array of values
* @param i an index
* @param j another index
*/
private static void exch(long[] values, int i, int j){
long k = values[i];
values[i] = values[j];
values[j] = k;
} | /storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java |
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