id stringlengths 25 27 | content stringlengths 190 15.4k | max_stars_repo_path stringlengths 31 217 |
|---|---|---|
robustness-copilot_data_401 | /**
* Create CollectionMembership relationships between a Process asset and a Collection. Verifies that the
* relationship is not present before creating it
*
* @param userId the name of the calling user
* @param processGUID the unique identifier of the process
* @param ... | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineCollectionHandler.java |
robustness-copilot_data_402 | /**
* Helper method for finding wrapper type for given primitive type (why isn't
* there one in JDK?).
* NOTE: throws {@link IllegalArgumentException} if given type is NOT primitive
* type (caller has to check).
*/
public static Class<?> wrapperType(Class<?> primitiveType){
if (primitiveTy... | /src/main/java/com/fasterxml/jackson/databind/util/ClassUtil.java |
robustness-copilot_data_403 | /**
* Checks if the agent has a valid dispatcher headers.
*
* @param agent Agent to check
* @return true if the Agent's headers contain the proper values
*/
private boolean isDispatcherHeaders(final Agent agent){
final ValueMap properties = agent.getConfiguration().getProperties();
fin... | /bundle/src/main/java/com/adobe/acs/commons/replication/dispatcher/DispatcherFlushFilter.java |
robustness-copilot_data_404 | /**
* Checks if the find possible distance is the minimal one.
*
* @param minimalAdditionalDistance
* @param possibleAdditionalDistance
* @return the minimal transport distance
*/
private double findMinimalDistance(double minimalAdditionalDistance, double possibleAdditionalDistance){
if (minimalAdditio... | /contribs/freight/src/main/java/org/matsim/contrib/freight/jsprit/DistanceConstraint.java |
robustness-copilot_data_405 | /**
* Returns a one line string representation of this Container. This method is
* conform RFC #9.
*
* @return The string representation of this Container
*/
public String toString(){
StringBuffer resultString = new StringBuffer(32);
resultString.append("Bond(").append(this.hashCode())... | /base/silent/src/main/java/org/openscience/cdk/silent/Bond.java |
robustness-copilot_data_406 | /**
* Utility for find the first directional edge incident to a vertex. If
* there are no directional labels then null is returned.
*
* @param g graph from Beam
* @param u the vertex for which to find
* @return first directional edge (or null if none)
*/
private Edge findDirectionalE... | /storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java |
robustness-copilot_data_407 | /**
* Returns true if the specified YAML string matches this configuration, ignoring unknown fields
* and field ordering. Note that ordering of elements in arrays is considered significant for this comparison.
* @param yaml a monitoring exporter configuration to compare to this object.
*/
public boolean ma... | /operator/src/main/java/oracle/kubernetes/weblogic/domain/model/MonitoringExporterConfiguration.java |
robustness-copilot_data_408 | /** Returns the natural log of the values in this column as a NumberColumn. */
DoubleColumn logN(){
DoubleColumn newColumn = DoubleColumn.create(name() + "[logN]", size());
for (int i = 0; i < size(); i++) {
newColumn.set(i, Math.log(getDouble(i)));
}
return newColumn;
} | /core/src/main/java/tech/tablesaw/columns/numbers/NumberMapFunctions.java |
robustness-copilot_data_409 | /**
* Returns a StringColumn with the year and day-of-year derived from this column concatenated into
* a String that will sort lexicographically in temporal order.
*
* <p>This simplifies the production of plots and tables that aggregate values into standard
* temporal units (e.g., you want monthly data ... | /core/src/main/java/tech/tablesaw/columns/datetimes/DateTimeMapFunctions.java |
robustness-copilot_data_410 | /**
* The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
*
*@param atom The IAtom for which the DescriptorValue is requested
... | /descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java |
robustness-copilot_data_411 | /**
* CTfile specification is ambiguous as to how parity values should be written
* for implicit hydrogens. Old applications (Symyx Draw) seem to push any
* hydrogen to (implied) the last position but newer applications
* (Accelrys/BioVia Draw) only do so for implicit hydrogens (makes more sense).
... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java |
robustness-copilot_data_412 | /**
* Factory method for constructing a simple transformer based on
* prefix and/or suffix.
*/
public static NameTransformer simpleTransformer(final String prefix, final String suffix){
boolean hasPrefix = (prefix != null) && !prefix.isEmpty();
boolean hasSuffix = (suffix != null) && !suffix.isE... | /src/main/java/com/fasterxml/jackson/databind/util/NameTransformer.java |
robustness-copilot_data_413 | /**
* Converts a number like 1634 to the time value of 16:34:00.
*
* @param hhmm the time-representing number to convert.
* @return the time as seconds after midnight.
*/
public static double convertHHMMInteger(int hhmm){
int h = hhmm / 100;
int m = hhmm - (h * 100);
double seconds = Math.abs(h)... | /matsim/src/main/java/org/matsim/core/utils/misc/Time.java |
robustness-copilot_data_414 | /**
* Get bond order value as {@code int} value.
*
* @param bond The {@link IBond} for which the order is returned.
* @return 1 for a single bond, 2 for a double bond, 3 for a triple bond, 4 for a quadruple bond,
* and 0 for any other bond type.
*/
public static int con... | /legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java |
robustness-copilot_data_415 | /**
* Read topics of TREC Microblog Tracks from 2011 to 2014 including:
* topics.microblog2011.txt
* topics.microblog2012.txt
* topics.microblog2013.txt
* topics.microblog2014.txt
* @return SortedMap where keys are query/topic IDs and values are title portions of the topics
* @throws IOException an... | /src/main/java/io/anserini/search/topicreader/MicroblogTopicReader.java |
robustness-copilot_data_416 | /**
* Copies the content from one stream to another stream.
*
* @param fromStream The stream containing the data to be copied
* @param toStream The stream the data should be written to
*
* @throws UncheckedIOException
*/
public static void copyStream(final InputStream fromStream, final OutputStream to... | /matsim/src/main/java/org/matsim/core/utils/io/IOUtils.java |
robustness-copilot_data_417 | /**
* Appends a placeholder indicating that some frames were not written.
*/
private void appendPlaceHolder(StringBuilder builder, int indent, int consecutiveExcluded, String message){
indent(builder, indent);
builder.append(ELLIPSIS).append(" ").append(consecutiveExcluded).append(" ").append(message... | /src/main/java/net/logstash/logback/stacktrace/ShortenedThrowableConverter.java |
robustness-copilot_data_418 | /**
* Adds all the commonly used config-groups, also known as "core modules",
* to this config-instance. This should be called before reading any
* configuration from file.
*/
public void addCoreModules(){
this.global = new GlobalConfigGroup();
this.modules.put(GlobalConfigGroup.GROUP_NAME, this.global... | /matsim/src/main/java/org/matsim/core/config/Config.java |
robustness-copilot_data_419 | /**
* Create an encoder for the {@link IDoubleBondStereochemistry} element.
*
* @param dbs stereo element from an atom container
* @param atomToIndex map of atoms to indices
* @param graph adjacency list of connected vertices
* @return a new geometry encoder
*/
priva... | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java |
robustness-copilot_data_420 | /**
* Given vectors for the hypotenuse and adjacent side of a right angled
* triangle and the length of the opposite side, determine how long the
* adjacent side size.
*
* @param hypotenuse vector for the hypotenuse
* @param adjacent vector for the adjacent side
* @param oppositeLengt... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/VecmathUtil.java |
robustness-copilot_data_421 | /**
* Validate that we can connect to the new SSL certificate posted on api.twilio.com.
*
* @throws CertificateValidationException if the connection fails
*/
public static void validateSslCertificate(){
final NetworkHttpClient client = new NetworkHttpClient();
final Request request = new Re... | /src/main/java/com/twilio/Twilio.java |
robustness-copilot_data_422 | /**
* Open a property file that is embedded as a Java resource and parse it.
*
* @param potentialPropertyFile location and file name of the property file
* @throws IOException if the file cannot be opened
* @throws CommandLineParsingException if an error occurs during parsing
... | /liquibase-core/src/main/java/liquibase/integration/commandline/Main.java |
robustness-copilot_data_423 | /**
* Invoke the specified visitor function for every schema that matches mimeType in the OpenAPI document.
*
* To avoid infinite recursion, referenced schemas are visited only once. When a referenced schema is visited,
* it is added to visitedSchemas.
*
* @param openAPI the OpenAPI docume... | /modules/openapi-generator/src/main/java/org/openapitools/codegen/utils/ModelUtils.java |
robustness-copilot_data_424 | /**
* Returns a table with n by m + 1 cells. The first column contains labels, the other cells
* contains the counts for every unique combination of values from the two specified columns in
* this table.
*/
public Table xTabCounts(String column1Name, String column2Name){
return CrossTab.counts(this, ca... | /core/src/main/java/tech/tablesaw/api/Table.java |
robustness-copilot_data_425 | /**
* Convert a CDK {@link IBond} to the Beam edge label type.
*
* @param b cdk bond
* @return the edge label for the Beam edge
* @throws NullPointerException the bond order was null and the bond was
* not-aromatic
* @throws IllegalArgumentExceptio... | /storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java |
robustness-copilot_data_426 | /**
* Create a new CDK {@link IAtom} from the Beam Atom.
*
* @param beamAtom an Atom from the Beam ChemicalGraph
* @param hCount hydrogen count for the atom
* @return the CDK atom to have it's properties set
*/
IAtom toCDKAtom(Atom beamAtom, int hCount){
IAtom cdkAtom = newCDKAtom(b... | /storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java |
robustness-copilot_data_427 | /**
* Create an index of atoms for the provided {@code container}.
*
* @param container the container to index the atoms of
* @return the index/lookup of atoms to the index they appear
*/
private static Map<IAtom, Integer> indexAtoms(IAtomContainer container){
Map<IAtom, Integer> map = new... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java |
robustness-copilot_data_428 | /**
* Calculates the Fsp<sup>3</sup> descriptor value for the given {@link IAtomContainer}.
*
* @param mol An {@link org.openscience.cdk.interfaces.IAtomContainer} for which this descriptor
* should be calculated
* @return An object of {@link org.openscience.cdk.qsar.DescriptorValue}... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalCSP3Descriptor.java |
robustness-copilot_data_429 | /**
* Update the resource with the properties from the row.
*
* @param resource Resource object of which the properties are to be modified.
* @param nodeInfo Map of properties from the row.
*/
private void populateMetadataFromRow(Resource resource, Map<String, Object> nodeInfo) throws Reposito... | /bundle/src/main/java/com/adobe/acs/commons/mcp/impl/processes/DataImporter.java |
robustness-copilot_data_430 | /**
* Parses the list of character rules as defined in the database. Recall how
* configString is formatted: "UpperCase:1,LowerCase:1,Digit:1,Special:1"
*/
public static List<CharacterRule> parseConfigString(String configString){
List<CharacterRule> characterRules = new ArrayList<>();
String[] t... | /src/main/java/edu/harvard/iq/dataverse/validation/PasswordValidatorUtil.java |
robustness-copilot_data_431 | /**
* Create a pattern for the provided SMARTS - if the SMARTS is '?' a pattern
* is not created.
*
* @param smarts a smarts pattern
* @param builder chem object builder
* @return the pattern to match
*/
private Pattern createPattern(String smarts, IChemObjectBuilder builder) throws... | /descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/MACCSFingerprinter.java |
robustness-copilot_data_432 | /**
* Since durations were added later there is need to fill missing data for those statuses.
*/
private void fillMissingDurations(){
long[] extendedArray = new long[buildNumbers.length];
Arrays.fill(extendedArray, -1);
System.arraycopy(durations, 0, extendedArray, buildNumbers.length - durations... | /src/main/java/net/masterthought/cucumber/Trends.java |
robustness-copilot_data_433 | /**
* Generate valid days of the month for the days of week expression. This method requires that you
* pass it a -1 for the reference value when starting to generate a sequence of day values. That allows
* it to handle the special case of which day of the month is the initial matching value.
*
... | /src/main/java/com/cronutils/model/time/generator/OnDayOfWeekValueGenerator.java |
robustness-copilot_data_434 | /**
* Add data from a given CodegenModel that the oneOf implementor should implement. For example:
*
* @param cm model that the implementor should implement
* @param modelsImports imports of the given `cm`
*/
public void addFromInterfaceModel(CodegenModel cm, List<Map<String, String>> modelsIm... | /modules/openapi-generator/src/main/java/org/openapitools/codegen/utils/OneOfImplementorAdditionalData.java |
robustness-copilot_data_435 | /**
* Given a bond length for a model, calculate the scale that will transform
* this length to the on screen bond length in RendererModel.
*
* @param modelBondLength the average bond length of the model
* @return the scale necessary to transform this to a screen bond
*/
public double cal... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/AtomContainerRenderer.java |
robustness-copilot_data_436 | /**
* Method that subclasses may call for standard handling of an exception thrown when
* calling constructor or factory method. Will unwrap {@link ExceptionInInitializerError}
* and {@link InvocationTargetException}s, then call {@link #wrapAsJsonMappingException}.
*
* @since 2.7
*/
prote... | /src/main/java/com/fasterxml/jackson/databind/deser/std/StdValueInstantiator.java |
robustness-copilot_data_437 | /**
* Find out if the SchemaType 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 schema type to be searched
*
* @return optional wi... | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineSchemaTypeHandler.java |
robustness-copilot_data_438 | /**
* Sum the components of two vectors, the input is not modified.
*
* @param a first vector
* @param b second vector
* @return scaled vector
*/
static Vector2d sum(final Tuple2d a, final Tuple2d b){
return new Vector2d(a.x + b.x, a.y + b.y);
} | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/VecmathUtil.java |
robustness-copilot_data_439 | /**
* Will not commit the response, but only make sure that the wrapped response's {@code flushBuffer()} is executed, once this {@link #close()} is called.
* This only affects output which is buffered, i.e. for unbuffered output the flush is not deferred.
* @throws IOException
*/
public void flush... | /bundle/src/main/java/com/adobe/acs/commons/util/BufferedServletOutput.java |
robustness-copilot_data_440 | /**
* Updates the last status reported for the specified server.
*
* @param serverName the name of the server
* @param status the new status
*/
public void updateLastKnownServerStatus(String serverName, String status){
getSko(serverName).getLastKnownStatus().getAndUpdate(lastKnownStatus -> {
... | /operator/src/main/java/oracle/kubernetes/operator/helpers/DomainPresenceInfo.java |
robustness-copilot_data_441 | /**
* Check if the type of the JsonNode's value is number based on the
* status of typeLoose flag.
*
* @param node the JsonNode to check
* @param config the SchemaValidatorsConfig to depend on
* @return boolean to indicate if it is a number
*/
public static boolean isNumb... | /src/main/java/com/networknt/schema/TypeValidator.java |
robustness-copilot_data_442 | /**
* By snapping to the cardinal direction (compass point) of the provided
* vector, return the position opposite the 'snapped' coordinate.
*
* @param opposite position the hydrogen label opposite to this vector
* @return the position
*/
static HydrogenPosition usingCardinalDirection(fin... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java |
robustness-copilot_data_443 | /**
* Transforms a point according to the current affine transformation,
* converting a world coordinate into a screen coordinate.
*
* @param xCoord x-coordinate of the world point to transform
* @param yCoord y-coordinate of the world point to transform
* @return the transformed scr... | /display/renderawt/src/main/java/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java |
robustness-copilot_data_444 | /**
* Quick check to see whether <i>both</i> the links are shorter than the
* given threshold.
* @param linkA
* @param linkB
* @param thresholdLength
* @return true if <i>both</i> links are shorter than the given threshold,
* false otherwise.
*/
private boolean bothLinksAreShorterThanThreshold(Link ... | /matsim/src/main/java/org/matsim/core/network/algorithms/NetworkSimplifier.java |
robustness-copilot_data_445 | /**
* Labels the atom at the specified index with the provide label. If the
* atom was not already a pseudo atom then the original atom is replaced.
*
* @param container structure
* @param index atom index to replace
* @param label the label for the atom
* @see IPseudoAtom#set... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java |
robustness-copilot_data_446 | /**
* Index the stereo elements of the {@code container} into the the {@code
* elements} and {@code types} arrays. The {@code map} is used for looking
* up the index of atoms.
*
* @param map index of atoms
* @param elements array to fill with stereo elements
* @param types ... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java |
robustness-copilot_data_447 | /**
* Execute all numbering functions for the given slice setting values in the appropriate
* destination column.
*/
private void processNumberingFunctions(TableSlice slice){
for (String toColumn : query.getArgumentList().getNumberingFunctions().keySet()) {
if (rowComparator == null) {
... | /core/src/main/java/tech/tablesaw/analytic/AnalyticQueryEngine.java |
robustness-copilot_data_448 | /**
* Loads all mandatory Scenario elements and
* if activated in config's scenario module/group
* optional elements.
* @return the Scenario
*/
Scenario loadScenario(){
// String currentDir = new File("tmp").getAbsolutePath();
// currentDir = currentDir.substring(0, currentDir.length() - 3);
// l... | /matsim/src/main/java/org/matsim/core/scenario/ScenarioLoaderImpl.java |
robustness-copilot_data_449 | /**
* This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
*
* @param list The list produced by the getMap method.
* @param sourceGraph The first atom container. Must not be atom IQueryAtomContainer.
* @param target... | /legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCS.java |
robustness-copilot_data_450 | /**
* Check the validity of the parameters received for this activation.
*
* @param action The replication action specifying properties of the activation.
* @param path The path to the item to be activated.
* @throws ReplicationException Throws a replication exception if invalid.
*/
priva... | /bundle/src/main/java/com/adobe/acs/commons/replication/dispatcher/impl/RefetchFlushContentBuilderImpl.java |
robustness-copilot_data_451 | /**
* Check to see if this permutation is the identity permutation.
*
* @return true if for all i, p[i] = i
*/
public boolean isIdentity(){
for (int i = 0; i < this.values.length; i++) {
if (this.values[i] != i) {
return false;
}
}
return true;
} | /tool/group/src/main/java/org/openscience/cdk/group/Permutation.java |
robustness-copilot_data_452 | /**
* Adds the specified element to this priority queue, with the given priority.
* @param o
* @param priority
* @return <tt>true</tt> if the element was added to the collection.
*/
public boolean add(final E o, final double priority){
if (o == null) {
throw new NullPointerException();
}
... | /matsim/src/main/java/org/matsim/core/utils/collections/PseudoRemovePriorityQueue.java |
robustness-copilot_data_453 | /**
* Overriding `adaptTo` to avoid using the original request as the adaptable.
*/
public AdapterType adaptTo(Class<AdapterType> type){
AdapterType result = null;
synchronized (this) {
result = (AdapterType) this.adaptersCache.get(type);
if (result == null) {
AdapterManag... | /bundle/src/main/java/com/adobe/acs/commons/util/OverridePathSlingRequestWrapper.java |
robustness-copilot_data_454 | /**
* Returns true if the two maps of values match. A null map is considered to match an empty map.
*
* @param first the first map to compare
* @param second the second map to compare
* @return true if the maps match.
*/
static boolean mapEquals(Map<K, V> first, Map<K, V> second){
return Object... | /operator/src/main/java/oracle/kubernetes/operator/helpers/KubernetesUtils.java |
robustness-copilot_data_455 | /**
* Converts an array of Regex strings into compiled Patterns.
*
* @param regexes the regex strings to compile into Patterns
* @return the list of compiled Patterns
*/
private List<Pattern> compileToPatterns(final List<String> regexes){
final List<Pattern> patterns = new ArrayList<Patter... | /bundle/src/main/java/com/adobe/acs/commons/httpcache/config/impl/HttpCacheConfigImpl.java |
robustness-copilot_data_456 | /**
* Evaluate the LINGO similarity between two key,value sty;e fingerprints.
*
* The value will range from 0.0 to 1.0.
*
* @param features1
* @param features2
* @return similarity
*/
public static float calculate(Map<String, Integer> features1, Map<String, Integer> features2){
... | /descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/LingoSimilarity.java |
robustness-copilot_data_457 | /**
* Access continue field, if any, from list metadata.
* @param result Kubernetes list result
* @return Continue value
*/
public static String accessContinue(Object result){
return Optional.ofNullable(result).filter(KubernetesListObject.class::isInstance).map(KubernetesListObject.class::cast).map(Kub... | /operator/src/main/java/oracle/kubernetes/operator/calls/AsyncRequestStep.java |
robustness-copilot_data_458 | /**
* Checks if the atom can be involved in a double-bond.
* @param idx atom idx
* @return the atom at index (idx) is valid for a double bond
* @see <a href="http://www.inchi-trust.org/download/104/InChI_TechMan.pdf">Double bond stereochemistry, InChI Technical Manual</a>
*/
private boolean is... | /tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java |
robustness-copilot_data_459 | /**
* Create an instance of a {@link ValidationRule} which should result in a warning should the evaluate of this rule fail.
*
* @param description A description to help differentiate this rule from others (not intended to be user-facing).
* @param failureMessage The message to be displayed in the e... | /modules/openapi-generator-core/src/main/java/org/openapitools/codegen/validation/ValidationRule.java |
robustness-copilot_data_460 | /**
* Sort solution by ascending order of the fragment count.
*/
public synchronized void sortResultsByFragments(){
Map<Integer, Map<Integer, Integer>> allFragmentMCS = new TreeMap<Integer, Map<Integer, Integer>>();
Map<Integer, Map<IAtom, IAtom>> allFragmentAtomMCS = new TreeMap<Integer, Map<IAtom, ... | /legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java |
robustness-copilot_data_461 | /**
* Executes the health check, catching and handling any exceptions raised by {@link #check()}.
*
* @return if the component is healthy, a healthy {@link Result}; otherwise, an unhealthy {@link
* Result} with a descriptive error message or exception
*/
Result execute(){
long start = clo... | /metrics-healthchecks/src/main/java/io/dropwizard/metrics5/health/HealthCheck.java |
robustness-copilot_data_462 | /**
* Creates empty columns that will be filled in when the analytic aggregate or numbering functions
* are executed.
*/
private void addColumns(){
this.destination.addColumns(query.getArgumentList().createEmptyDestinationColumns(query.getTable().rowCount()).toArray(new Column<?>[0]));
} | /core/src/main/java/tech/tablesaw/analytic/AnalyticQueryEngine.java |
robustness-copilot_data_463 | /**
* Assign a 2D layout to the atom container using the contents of the library. If multiple
* coordinates are available the first is choosen.
*
* @param container structure representation
* @return a layout was assigned
*/
boolean assignLayout(IAtomContainer container){
try {
... | /tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java |
robustness-copilot_data_464 | /**
* Execute the ImageTransformers as specified by the Request's suffix segments against the Image layer.
*
* @param layer the Image layer
* @param imageTransformersWithParams the transforms and their params
* @return the transformed Image layer
*/
protected final Layer transform(Layer l... | /bundle/src/main/java/com/adobe/acs/commons/images/impl/NamedTransformImageServlet.java |
robustness-copilot_data_465 | /**
* Returns a Pattern for matching the provided billing format.
* <p>
* Attributes are turned into named capturing groups.
*/
private static Pattern toPattern(String name, String format){
StringBuilder regex = new StringBuilder();
Matcher matcher = ATTRIBUTE_PATTERN.matcher(format);
i... | /modules/dcache/src/main/java/org/dcache/services/billing/text/BillingParserBuilder.java |
robustness-copilot_data_466 | /**
* Returns true if the current map is missing values from the required map. This method is
* typically used to compare labels and annotations against specifications derived from the
* domain.
*
* @param current a map of the values found in a Kubernetes resource
* @param required a map of the value... | /operator/src/main/java/oracle/kubernetes/operator/helpers/KubernetesUtils.java |
robustness-copilot_data_467 | /**
* Returns true if the given atom participates in this bond.
*
* @param atom The atom to be tested if it participates in this bond
* @return true if the atom participates in this bond
*/
public boolean contains(IAtom atom){
if (atoms == null)
return false;
for (IAtom localAt... | /base/silent/src/main/java/org/openscience/cdk/silent/Bond.java |
robustness-copilot_data_468 | /**
* Maps the function across all rows, storing the results into the provided Column.
*
* <p>The target column must have at least the same number of rows.
*
* @param fun function to map
* @param into Column into which results are set
* @return the provided Column
*/
C mapInto(Function<? super ... | /core/src/main/java/tech/tablesaw/columns/Column.java |
robustness-copilot_data_469 | /**
* Get set of attributes extracted from the search result.
*
* @param <T> type of extracted type.
* @param sre ldap search result.
* @param attr search result attribute.
* @param mapper mapping function to apply to each result element.
* @return set of attributes.
* @t... | /modules/gplazma2-ldap/src/main/java/org/dcache/gplazma/plugins/Ldap.java |
robustness-copilot_data_470 | /**
* Refines the coarse partition <code>a</code> into a finer one.
*
* @param coarser the partition to refine
* @return a finer partition
*/
public Partition refine(Partition coarser){
Partition finer = new Partition(coarser);
blocksToRefine = new LinkedList<Set<Integer>>();
for (... | /tool/group/src/main/java/org/openscience/cdk/group/EquitablePartitionRefiner.java |
robustness-copilot_data_471 | /**
* Read a <code>ChemFile</code> from a file in PDB format. The molecules
* in the file are stored as <code>BioPolymer</code>s in the
* <code>ChemFile</code>. The residues are the monomers of the
* <code>BioPolymer</code>, and their names are the concatenation of the
* residue, chain id, and ... | /storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java |
robustness-copilot_data_472 | /**
* Calculates the topological polar surface area and expresses it as a ratio to molecule size.
*
* @param mol The {@link IAtomContainer} whose volume is to be calculated
* @return descriptor(s) retaining to polar surface area
*/
public DescriptorValue calculate(IAtomContainer mol){
try ... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalPSADescriptor.java |
robustness-copilot_data_473 | /**
* Get a list of all Elements which are contained
* molecular.
*
*@param formula The MolecularFormula to check
*@return The list with the IElements in this molecular formula
*/
public static List<IElement> elements(IMolecularFormula formula){
List<IElement> elementList... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_474 | /**
* Adds an carrierVehicle to the CarrierCapabilites of the Carrier.
* @param carrier
* @param carrierVehicle
*/
public static void addCarrierVehicle(Carrier carrier, CarrierVehicle carrierVehicle){
carrier.getCarrierCapabilities().getCarrierVehicles().put(carrierVehicle.getId(), carrierVehicle);
} | /contribs/freight/src/main/java/org/matsim/contrib/freight/carrier/CarrierUtils.java |
robustness-copilot_data_475 | /**
* Whether this cluster contains a server with the given server name,
* including servers that are both configured and dynamic servers.
*
* @param serverName server name to be checked
* @return True if the cluster contains a server with the given server name
*/
boolean containsServer(@Nonnull Str... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsClusterConfig.java |
robustness-copilot_data_476 | /**
* Creates an <code>Atom</code> and sets properties to their values from
* the ATOM or HETATM record. If the line is shorter than 80 characters, the
* information past 59 characters is treated as optional. If the line is
* shorter than 59 characters, a <code>RuntimeException</code> is thrown.
... | /storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java |
robustness-copilot_data_477 | /**
* This function checks whether our parent should expunge us.
*/
public boolean hasExpired(){
Date now = new Date();
return _whenIShouldExpire != null ? !now.before(_whenIShouldExpire) : false;
} | /modules/dcache-info/src/main/java/org/dcache/services/info/base/StateComposite.java |
robustness-copilot_data_478 | /**
* Ensures the node's primary type is included in the Included Node Types and NOT in the Excluded Node Types and NOT in the Excluded Node Names.
*
* @param node the candidate node
* @param options the checksum options containing the included and excluded none types
* @return true if the n... | /bundle/src/main/java/com/adobe/acs/commons/analysis/jcrchecksum/impl/ChecksumGeneratorImpl.java |
robustness-copilot_data_479 | /**
* Check whether otherPath points to the same location, or is a child of this path. This is
* true iff each element of this path is identical to the corresponding element in otherPath.
* <pre>
* StatePath p1 = new StatePath("foo.bar");
* StatePath p2 = new StatePath("foo.bar.baz");
*... | /modules/dcache-info/src/main/java/org/dcache/services/info/base/StatePath.java |
robustness-copilot_data_480 | /**
* Helper method for constructing a new array that contains specified
* element followed by contents of the given array but never contains
* duplicates.
* If element already existed, one of two things happens: if the element
* was already the first one in array, array is returned as is; but
... | /src/main/java/com/fasterxml/jackson/databind/util/ArrayBuilders.java |
robustness-copilot_data_481 | /**
* Checks a list of new data files for duplicate names, renaming any
* duplicates to ensure that they are unique.
*
* @param version the dataset version
* @param newFiles the list of new data files to add to it
* @param fileToReplace
*/
public static void checkForDuplicateFileName... | /src/main/java/edu/harvard/iq/dataverse/ingest/IngestUtil.java |
robustness-copilot_data_482 | /**
* Check whether the url is supported to extract or not.
*
* @param appURL app url
* @return true is the url supported, otherwise not
*/
public static boolean isExtraction(final String appURL){
for (String each : EXTRACTION_TYPES) {
if (appURL.endsWith(each)) {
retur... | /elasticjob-cloud/elasticjob-cloud-scheduler/src/main/java/org/apache/shardingsphere/elasticjob/cloud/scheduler/mesos/SupportedExtractionType.java |
robustness-copilot_data_483 | /**
* Add a new component to our list of children.
* <p>
*
* @param childName the name under which this item should be recorded
* @param newChild the StateComponent to be stored.
*/
private void addComponent(String childName, StateComponent newChild){
StateComponent existingChild = _... | /modules/dcache-info/src/main/java/org/dcache/services/info/base/StateComposite.java |
robustness-copilot_data_484 | /**
* Method that actually does the work of extracting the molecular formula.
*
* @param mass molecular formula to create from the mass
* @return the filled molecular formulas as IMolecularFormulaSet
*/
public IMolecularFormulaSet generate(double mass){
if (mass... | /legacy/src/main/java/org/openscience/cdk/formula/MassToFormulaTool.java |
robustness-copilot_data_485 | /**
* Removes a particular strand, specified by its name.
*
* @param name name of the strand to remove
*/
public void removeStrand(String name){
if (strands.containsKey(name)) {
Strand strand = (Strand) strands.get(name);
this.remove(strand);
strands.remove(name);
}
... | /base/silent/src/main/java/org/openscience/cdk/silent/BioPolymer.java |
robustness-copilot_data_486 | /**
* Checks whether the query distance constraint matches a target distance.
*
* This method checks whether a query constraint is satisfied by an observed
* distance (represented by a {@link PharmacophoreBond} in the target molecule.
* Note that distance are compared upto 2 decimal places.
... | /tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryBond.java |
robustness-copilot_data_487 | /**
* Distribute the bonded atoms (neighbours) of an atom such that they fill the
* remaining space around an atom in a geometrically nice way.
* IMPORTANT: This method is not supposed to handle the
* case of one or no place neighbor. In the case of
* one placed neigbor, the chain placemen... | /tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java |
robustness-copilot_data_488 | /**
* Returns true if the value in the field is required to be DNS-1123 legal.
*
* @param fieldName Name of the field to be checked
* @return true if the value needs to be DNS1123 legal, false otherwise
*/
public static boolean isDns1123Required(String fieldName){
if (fieldName != null) {
fo... | /operator/src/main/java/oracle/kubernetes/operator/helpers/LegalNames.java |
robustness-copilot_data_489 | /**
* Removes all trailing zero decimals from the given String, assuming all decimals are zero and
* any zero decimals actually exist.
*
* <p>A {@code null} input String returns {@code null}.
*
* @param str the String to handle, may be null
* @return string without trailing zero decimals
*/
pub... | /core/src/main/java/tech/tablesaw/util/StringUtils.java |
robustness-copilot_data_490 | /**
* Returns the topology equivalent of the domain configuration, as a map. It may be converted to
* YAML or JSON via an object mapper.
*
* @return a map containing the topology
*/
public Map<String, Object> toTopology(){
Map<String, Object> topology = new HashMap<>();
topology.put("domainValid... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsDomainConfig.java |
robustness-copilot_data_491 | /**
* Generate an {@link OpenAPI} model from Jooby class. This method parses class byte code and
* generates an open api model from it. Compilation must be done with debug information and
* parameters name available.
*
* Optionally, the <code>conf/openapi.yaml</code> is used as template and get merged in... | /modules/jooby-openapi/src/main/java/io/jooby/openapi/OpenAPIGenerator.java |
robustness-copilot_data_492 | /**
* Computes the score of a document with respect to a query given a scoring function and an analyzer.
*
* @param reader index reader
* @param docid docid of the document to score
* @param q query
* @param similarity scoring function
* @param analyzer analyzer to use
* @return the score of the... | /src/main/java/io/anserini/index/IndexReaderUtils.java |
robustness-copilot_data_493 | /**
* Refines the compatibility removing any mappings which have now become
* invalid (since the last mapping). The matrix is refined from the row
* after the current {@code row} - all previous rows are fixed. If when
* refined we find a query vertex has no more candidates left in the target
* ... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java |
robustness-copilot_data_494 | /**
* Search and place branches of a chain or ring.
*
*@param chain AtomContainer if atoms in an aliphatic chain or ring system
*/
private void searchAndPlaceBranches(IAtomContainer molecule, IAtomContainer chain, AtomPlacer3D ap3d, AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPla... | /tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java |
robustness-copilot_data_495 | /**
* Default implementation, just look for "local" IPs. If the database returns a null URL we return false since we don't know it's safe to run the update.
*
* @throws liquibase.exception.DatabaseException
*
*/
public boolean isSafeToRunUpdate() throws DatabaseException{
DatabaseConnectio... | /liquibase-core/src/main/java/liquibase/database/AbstractJdbcDatabase.java |
robustness-copilot_data_496 | /**
* Returns a lexicographically sorted map of the [PROPERTY PATH] : [CHECKSUM OF PROPERTIES].
* @param aggregateNodePath the absolute path of the node being aggregated into a checksum
* @param node the node to collect and checksum the properties for
* @param options the checksum generator options... | /bundle/src/main/java/com/adobe/acs/commons/analysis/jcrchecksum/impl/ChecksumGeneratorImpl.java |
robustness-copilot_data_497 | /**
* A convenience method for testing the value returned by {@link #getRequiredForDatabase()} against a given database.
* Returns true if the {@link Database#getShortName()} method is contained in the required databases or the
* required database list contains the string "all"
*/
public boolean is... | /liquibase-core/src/main/java/liquibase/change/ChangeParameterMetaData.java |
robustness-copilot_data_498 | /**
* Change the base of the group to the new base <code>newBase</code>.
*
* @param newBase the new base for the group
*/
public void changeBase(Permutation newBase){
PermutationGroup h = new PermutationGroup(newBase);
int firstDiffIndex = base.firstIndexOfDifference(newBase);
for (int ... | /tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java |
robustness-copilot_data_499 | /**
* Util for converting a String[] into a List of compiled Patterns. Empty/blank strings will be skipped.
* @param values the Strings to convert to patterns.
* @return a List of Patterns
*/
public static List<Pattern> toPatterns(String[] values){
List<Pattern> patterns = new ArrayList<Pattern... | /bundle/src/main/java/com/adobe/acs/commons/util/ParameterUtil.java |
robustness-copilot_data_500 | /**
* Looks at structural containment: whether {@code ra} is part of the
* group's structure. It mostly the same as {@link #contains(edu.harvard.iq.dataverse.engine.command.DataverseRequest)},
* except for logical containment. So if an ExplicitGroup contains {@link AuthenticatedUsers} but not
* a sp... | /src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroup.java |
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