id stringlengths 25 27 | content stringlengths 190 15.4k | max_stars_repo_path stringlengths 31 217 |
|---|---|---|
robustness-copilot_data_101 | /**
* Creates a new {@link Carriers} container only with {@link CarrierShipment}s
* for creating a new VRP. As consequence of the transformation of
* {@link CarrierService}s to {@link CarrierShipment}s the solution of the VRP
* can have tours with vehicles returning to the depot and ... | /contribs/freight/src/main/java/org/matsim/contrib/freight/utils/FreightUtils.java |
robustness-copilot_data_102 | /**
* Returns true if the first metadata indicates a newer resource than does the second. 'Newer'
* indicates that the creation time is later. If two items have the same creation time, a higher
* resource version indicates the newer resource.
*
* @param first the first item to compare
* @param second... | /operator/src/main/java/oracle/kubernetes/operator/helpers/KubernetesUtils.java |
robustness-copilot_data_103 | /**
* Create a pattern which can be used to find molecules which contain the
* {@code query} structure.
*
* @param query the substructure to find
* @return a pattern for finding the {@code query}
*/
public static Pattern findSubstructure(IAtomContainer query){
boolean isQuery = query ... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Ullmann.java |
robustness-copilot_data_104 | /**
* Creates a new CronDefinition instance with provided field definitions.
*
* @return returns CronDefinition instance, never null
*/
public CronDefinition instance(){
final Set<CronConstraint> validations = new HashSet<>();
validations.addAll(cronConstraints);
final List<FieldDefinit... | /src/main/java/com/cronutils/model/definition/CronDefinitionBuilder.java |
robustness-copilot_data_105 | /**
* Check if the specified access token can be authenticated.
*
* @param principal The user, group or service account.
* @param token The access token that identifies the user.
* @param namespace Namespace
* @return V1TokenReviewStatus containing either info about the authenticated user or an error
... | /operator/src/main/java/oracle/kubernetes/operator/helpers/AuthenticationProxy.java |
robustness-copilot_data_106 | /**
* Un-sign a value, previously signed with {@link #sign(String, String)}.
* Produces a nonnull value or <code>null</code> for invalid.
*
* @param value A signed value.
* @param secret A secret key.
* @return A new signed value or null.
*/
public static String unsign(@Nonnull final String value,... | /jooby/src/main/java/io/jooby/Cookie.java |
robustness-copilot_data_107 | /**
* kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
* @param molecule The {@link IAtomContainer} to kekulise
* @return The {@link IAtomContainer} with kekule structure
* @throws CDKExc... | /legacy/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java |
robustness-copilot_data_108 | /**
* Creates a step to initiate processing for all servers in the domain for which a configuration is defined,
* checking the configuration of each exporter sidecar and updating it if necessary.
*
* Expects packet to contain DomainPresenceInfo and:
* DOMAIN_TOPOLOGY the domain configura... | /operator/src/main/java/oracle/kubernetes/operator/steps/MonitoringExporterSteps.java |
robustness-copilot_data_109 | /**
* Helper method for adding isotope distributions to a MF. The method adds
* a distribution of isotopes by splitting the set of isotopes in two,
* the one under consideration (specified by 'idx') and the remaining to be
* considered ('>idx'). The inflection point is calculate as 'k'
* &le... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_110 | /**
* Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X
* system. (2) 2 ligands(B, C) of refAtom A (i) 1 points required; vector in
* ABC plane bisecting AB, AC. If ABC is linear, no points (ii) 2 points: 2
* points X1, X2, X1-A-X2 = angle about 2i vector
*
*@param aPoi... | /tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java |
robustness-copilot_data_111 | /**
* Possibly update our belief of the earliest time that a Mortal child StateComponent will
* expire. It is safe to call this method with all child Dates: it will update the
* _earliestChildExpiry Date correctly.
*
* @param newDate the expiry Date of a Mortal child StateComponent
*/
pr... | /modules/dcache-info/src/main/java/org/dcache/services/info/base/StateComposite.java |
robustness-copilot_data_112 | /**
* Using an import map created via {@link #getAllImportsMappings(Set)} to build a list import objects.
* The import objects have two keys: import and classname which hold the key and value of the initial map entry.
*
* @param mappedImports Map of fully qualified import and import
* @return T... | /modules/openapi-generator/src/main/java/org/openapitools/codegen/DefaultGenerator.java |
robustness-copilot_data_113 | /**
* Find out if the Transformation Project object is already stored in the repository as a Collection. 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
*
... | /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_114 | /**
* Check the feasibility of the candidate pair {n, m}. A candidate pair is
* syntactically feasible iff all k-look-ahead rules hold. These look ahead
* rules check adjacency relation of the mapping. If an edge is mapped in g1
* it should also be mapped in g2 and vise-versa (0-look-ahead). If an e... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VFState.java |
robustness-copilot_data_115 | /**
* Returns a table consisting of randomly selected records from this table. The sample size is
* based on the given proportion
*
* @param proportion The proportion to go in the sample
*/
public Table sampleX(double proportion){
Preconditions.checkArgument(proportion <= 1 && proportion >= 0, "The ... | /core/src/main/java/tech/tablesaw/api/Table.java |
robustness-copilot_data_116 | /**
* Creates the e-mail template parameter map and invokes the OSGi E-Mail Service.
*
* @param success the list of successful Health Check Execution Results
* @param failure the list of unsuccessful Health Check Execution Results
* @param timeTaken the time taken to execute all Health Checks
... | /bundle/src/main/java/com/adobe/acs/commons/hc/impl/HealthCheckStatusEmailer.java |
robustness-copilot_data_117 | /**
* If the hydrogens are position in from of the element we may need to move the hydrogen and
* hydrogen count labels. This code assesses the positions of the mass, hydrogen, and hydrogen
* count labels and determines the x-axis adjustment needed for the hydrogen label to dodge a
* collision.
... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java |
robustness-copilot_data_118 | /**
* Merges the values found in the the source properties into the destination
* property as a multi-value. The values of the source properties and
* destination properties must all be the same property type.
*
* The unique set of properties will be stored in
*
* @param resource the ... | /bundle/src/main/java/com/adobe/acs/commons/wcm/impl/PropertyMergePostProcessor.java |
robustness-copilot_data_119 | /**
* The method does not copy the message object - only the encoded message stream (if any).
*/
public CellMessage clone(){
try {
CellMessage copy = (CellMessage) super.clone();
copy._destination = _destination.clone();
if (_source != null) {
copy._source = _source.cl... | /modules/cells/src/main/java/dmg/cells/nucleus/CellMessage.java |
robustness-copilot_data_120 | /**
* Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
*
* @param enc The Base64 encoded fingerprint
* @return A BitSet corresponding to the input fingerprint
*/
public static BitSet decode(String enc){
byte[] fp = base64Decode(enc);
if (fp.length < 4) {
throw n... | /descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java |
robustness-copilot_data_121 | /**
* Provide download URL if no Terms of Use, no guestbook, and not
* restricted.
*/
public static boolean isPubliclyDownloadable(FileMetadata fileMetadata){
if (fileMetadata == null) {
return false;
}
if (fileMetadata.isRestricted()) {
String msg = "Not publicly downloadabl... | /src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java |
robustness-copilot_data_122 | /**
* Return a hash code based on the values of this object.
*
* @return in hash code
*/
public int hashCode(){
return Objects.hash(getType(), getInstanceProvenanceType(), getMetadataCollectionId(), getMetadataCollectionName(), getInstanceLicense(), getCreatedBy(), getUpdatedBy(), getCreateTime... | /open-metadata-implementation/repository-services/repository-services-apis/src/main/java/org/odpi/openmetadata/repositoryservices/connectors/stores/metadatacollectionstore/properties/instances/InstanceAuditHeader.java |
robustness-copilot_data_123 | /**
* Verify whether the WebLogic domain already has all the machines configured for use by the
* dynamic cluster. For example, if machineNamePrefix is "domain1-cluster1-machine" and
* numMachinesNeeded is 2, this method return true if machines named "domain1-cluster1-machine1"
* and "domain1-cluster1-machi... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsClusterConfig.java |
robustness-copilot_data_124 | /**
* Check if files in the certificate folders have been added or removed.
*/
boolean checkForChanges(){
final Map<File, byte[]> presents = new HashMap<>(fingerprints);
boolean modified = traverseDirectory(location, new IFileVisitor() {
@Override
public boolean visitFile(File file)... | /src/main/java/org/zeromq/ZCertStore.java |
robustness-copilot_data_125 | /**
* Create a stereo encoder for all potential 2D and 3D tetrahedral
* elements.
*
* @param container an atom container
* @param graph adjacency list representation of the container
* @return a new encoder for tetrahedral elements
*/
public StereoEncoder create(IAtomContainer co... | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactory.java |
robustness-copilot_data_126 | /**
* As it is possible that some implementations embed byte[] as POJONode
* (despite optimal being {@link BinaryNode}), let's add support for exposing
* binary data here too.
*/
public byte[] binaryValue() throws IOException{
if (_value instanceof byte[]) {
return (byte[]) _value;
... | /src/main/java/com/fasterxml/jackson/databind/node/POJONode.java |
robustness-copilot_data_127 | /**
* Checks whether both atoms are involved in an amide C-N bond: *N(*)C(*)=O.
*
* Only the most common constitution is considered. Tautomeric, O\C(*)=N\*,
* and charged forms, [O-]\C(*)=N\*, are ignored.
*
* @param atom0 the first bonding partner
* @param atom1 the second bonding pa... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java |
robustness-copilot_data_128 | /**
* Parse the json string containing WLS configuration and return a list containing a map of
* (server attribute name, attribute value).
*
* @param jsonString JSON string containing WLS configuration to be parsed
* @return a ParsedJson object containing WebLogic domain configuration by parsing the give... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsDomainConfig.java |
robustness-copilot_data_129 | /**
* Initialize a PatternLayout with the supplied format and throw an {@link IllegalArgumentException}
* if the format is invalid.
*
* @param format the pattern layout format
* @return a configured and started {@link PatternLayoutAdapter} instance around the supplied format
* @throws Ill... | /src/main/java/net/logstash/logback/pattern/AbstractJsonPatternParser.java |
robustness-copilot_data_130 | /**
* Converts a Lucene internal docid to a collection docid.
*
* @param reader index reader
* @param docid Lucene internal docid
* @return corresponding collection docid, or <code>null</code> if not found.
*/
public static String convertLuceneDocidToDocid(IndexReader reader, int docid){
if (doci... | /src/main/java/io/anserini/index/IndexReaderUtils.java |
robustness-copilot_data_131 | /**
* Generate a compact element for an atom, such as a circle or a square,
* rather than text element.
*
* @param atom the atom to generate the compact element for
* @param model the renderer model
* @return a compact rendering element
*/
public IRenderingElement generateCompactElem... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java |
robustness-copilot_data_132 | /**
* Retrieves and removes the head of this queue, or <tt>null</tt> if this
* queue is empty.
*
* @return the head of this queue, or <tt>null</tt> if this queue is empty.
*/
public E poll(){
E minValue;
if (isEmpty())
return null;
else {
this.m... | /matsim/src/main/java/org/matsim/core/router/priorityqueue/BinaryMinHeap.java |
robustness-copilot_data_133 | /**
* Find out if the DatabaseSchema 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 database schema to be searched
*
* @ret... | /open-metadata-implementation/access-services/data-engine/data-engine-server/src/main/java/org/odpi/openmetadata/accessservices/dataengine/server/handlers/DataEngineRelationalDataHandler.java |
robustness-copilot_data_134 | /**
* Used by {@link #sortMissingObjects(Collection, Database)} to determine whether to go into the sorting logic.
*/
protected boolean supportsSortingObjects(Database database){
return (database instanceof AbstractDb2Database) || (database instanceof MSSQLDatabase) || (database instanceof OracleDatabase... | /liquibase-core/src/main/java/liquibase/diff/output/changelog/DiffToChangeLog.java |
robustness-copilot_data_135 | /**
* Returns a Selection containing all values from totalRangeStart to totalRangeEnd, except for
* those in the range from excludedRangeStart to excludedRangeEnd. Start values are inclusive, end
* values exclusive.
*/
static Selection withoutRange(int totalRangeStart, int totalRangeEnd, int excludedRange... | /core/src/main/java/tech/tablesaw/selection/Selection.java |
robustness-copilot_data_136 | /**
* Whether the WebLogic domain contains a server with the given server name,
* including standalone servers, and servers that belong to a configured or dynamic cluster.
*
* @param serverName server name to be checked
* @return True if the WebLogic domain contains a server with the given server name
... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsDomainConfig.java |
robustness-copilot_data_137 | /**
* Recalculates the {@link LigancyFourChirality} based on the new, given atom ordering.
*
* @param newOrder new order of atoms
* @return the chirality following the new atom order
*/
public LigancyFourChirality project(ILigand[] newOrder){
ITetrahedralChirality.Stereo newStereo = this.s... | /descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/LigancyFourChirality.java |
robustness-copilot_data_138 | /**
* Appends a throwable and recursively appends its causedby/suppressed throwables
* in "reverse" order (Root cause first).
*/
private void appendRootCauseFirst(StringBuilder builder, String prefix, int indent, IThrowableProxy throwableProxy, Deque<String> stackHashes){
if (throwableProxy == null ... | /src/main/java/net/logstash/logback/stacktrace/ShortenedThrowableConverter.java |
robustness-copilot_data_139 | /**
* Find out if the relationship is already stored in the repository.
* It will search for relationships that have the source firstGUID and target secondGUID
*
* @param userId the name of the calling user
* @param firstGUID the unique identifier of the entity at first... | /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_140 | /**
* Invoke a method on an object and return whatever it returns.
*
* @param <T>
* the generic type
* @param method
* The method to invoke.
* @param object
* The instance or class (for static methods) on which to invoke the method.
* @param parameters
* ... | /src/main/java/org/apache/ibatis/io/VFS.java |
robustness-copilot_data_141 | /**
* Parse the "scope" claim and extract all SciToken or WLCG Profile scopes.
*/
private static List<AuthorisationSupplier> parseScope(String claim) throws InvalidScopeException{
return Splitter.on(' ').trimResults().splitToList(claim).stream().map(SciTokenPlugin::resolveScope).filter(Optional::isPresen... | /modules/gplazma2-scitoken/src/main/java/org/dcache/gplazma/scitoken/SciTokenPlugin.java |
robustness-copilot_data_142 | /**
* Flattens properties of inline object schemas that belong to a composed schema into a
* single flat list of properties. This is useful to generate a single or multiple
* inheritance model.
*
* In the example below, codegen may generate a 'Dog' class that extends from the
* generated '... | /modules/openapi-generator/src/main/java/org/openapitools/codegen/InlineModelResolver.java |
robustness-copilot_data_143 | /**
* Converts a {@link Resource} object into the matching {@link Order}.
*
* @param rdfOrder Resource for which the matching {@link Order} should be given.
* @return the matching {@link Order}.
*/
public static Order resource2Order(Resource rdfOrder){
if (rdfOrder.equals(CDK.SINGLEBOND)) ... | /storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java |
robustness-copilot_data_144 | /**
* Returns names of all attributes in the provided billing format.
*/
private static Set<String> toAttributes(String format){
Set<String> attributes = new HashSet<>();
Matcher matcher = ATTRIBUTE_PATTERN.matcher(format);
while (matcher.find()) {
String expression = matcher.group(1);
... | /modules/dcache/src/main/java/org/dcache/services/billing/text/BillingParserBuilder.java |
robustness-copilot_data_145 | /**
* Create or updates an external relationship between two entities. Verifies that the relationship is not present before creating it. If the
* relationship is present, verifies the instanceProperties for the relationship to be updated.
*
* @param userId the name of the calling use... | /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_146 | /**
* Obtain a prioritised array where the indices 0 to n which correspond to
* the provided {@code atoms}.
*
* @param focus focus of the tetrahedral atom
* @param atoms the atom
* @param n number of atoms
* @return prioritised indices
*/
private int[] priority(int focus, IA... | /tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java |
robustness-copilot_data_147 | /**
* Calculates the mass and abundance of all isotopes generated by adding one
* atom. Receives the periodic table element and calculate the isotopes, if
* there exist a previous calculation, add these new isotopes. In the
* process of adding the new isotopes, remove those that has an abundance
... | /tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternGenerator.java |
robustness-copilot_data_148 | /**
* Convenience method to perceive atom types for all <code>IAtom</code>s in the
* <code>IAtomContainer</code>, using the <code>CDKAtomTypeMatcher</code>. If the
* matcher finds atom matching atom type, the <code>IAtom</code> will be configured
* to have the same properties as the <code>IAtomType<... | /legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java |
robustness-copilot_data_149 | /**
* Checks whether the P atom is in a PO environment.
*
* This environment is noted in Kier & Hall (1986), page 20
*
* @param atom The P atom in question
* @param atomContainer The molecule containing the P atom
* @return The empirical delta V if present in the above envir... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java |
robustness-copilot_data_150 | /**
* Notifies registered listeners of certain changes that have occurred in
* this model.
*/
public void fireChange(){
if (getNotification() && listeners != null) {
EventObject event = new EventObject(this);
for (int i = 0; i < listeners.size(); i++) {
listeners.get(i).s... | /display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java |
robustness-copilot_data_151 | /**
* Partition the source table into a series of table slices. Does not modify the underlying table.
*/
private Iterable<TableSlice> partition(){
if (query.getPartitionColumns().isEmpty()) {
return ImmutableList.of(new TableSlice(query.getTable()));
}
return query.getTable().splitOn(query.ge... | /core/src/main/java/tech/tablesaw/analytic/AnalyticQueryEngine.java |
robustness-copilot_data_152 | /**
* Generate the whole group from the compact list of permutations.
*
* @return a list of permutations
*/
public List<Permutation> all(){
final List<Permutation> permutations = new ArrayList<Permutation>();
Backtracker counter = new Backtracker() {
@Override
public void a... | /tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java |
robustness-copilot_data_153 | /**
* Converts a {@link Model} into an {@link IAtomContainer} using the given {@link IChemObjectBuilder}.
*
* @param model RDF graph to deserialize into an {@link IAtomContainer}.
* @param builder {@link IChemObjectBuilder} used to create new {@link IChemObject}s.
* @return a {@link IAtomContai... | /storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java |
robustness-copilot_data_154 | /**
* Check whether redirection for the given request is allowed.
* <ol>
* <li>On author redirects are disabled in EDIT, PREVIEW and DESIGN WCM Modes.
* To test on author you need to disable WCM mode and append &wcmmode=disabled
* to the query string</li>
* <li>Redirects are supported only... | /bundle/src/main/java/com/adobe/acs/commons/redirects/filter/RedirectFilter.java |
robustness-copilot_data_155 | /**
* Returns the mappings between the reactant and the product side.
*
* @return An Iterator to the Mappings.
* @see #addMapping
*/
public Iterable<IMapping> mappings(){
return new Iterable<IMapping>() {
@Override
public Iterator<IMapping> iterator() {
retu... | /base/data/src/main/java/org/openscience/cdk/Reaction.java |
robustness-copilot_data_156 | /**
* Generates one or more SqlStatements depending on how the SQL should be parsed.
* If split statements is set to true then the SQL is split and each command is made into a separate SqlStatement.
* <p></p>
* If stripping comments is true then any comments are removed before the splitting is execu... | /liquibase-core/src/main/java/liquibase/change/AbstractSQLChange.java |
robustness-copilot_data_157 | /**
* Make a canonical signature string of a given height.
*
* @param height the maximum height to make signatures
* @return the canonical signature string
*/
public String toCanonicalSignatureString(int height){
String canonicalSignature = null;
for (int i = 0; i < getVertexCount(); i... | /descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeSignature.java |
robustness-copilot_data_158 | /**
* Create an encoder for the {@link ITetrahedralChirality} element.
*
* @param tc stereo element from an atom container
* @param atomToIndex map of atoms to indices
* @return a new geometry encoder
*/
private static GeometryEncoder encoder(ITetrahedralChirality tc, Map<IAtom, ... | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java |
robustness-copilot_data_159 | /**
* True, if the MolecularFormula contains the given element as IIsotope object.
*
* @param formula IMolecularFormula molecularFormula
* @param element The element this MolecularFormula is searched for
* @return True, if the MolecularFormula contains the given element object
... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_160 | /**
* Return the isotope pattern sorted by mass
* to the highest abundance.
*
* @param isotopeP The IsotopePattern object to sort
* @return The IsotopePattern sorted
*/
public static IsotopePattern sortByMass(IsotopePattern isotopeP){
try {
IsotopePattern isoSort = (... | /tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternManipulator.java |
robustness-copilot_data_161 | /**
* Calculates the distance based on the route-based distances between every tour
* activities. The method also integrates the associated pickup in the tour.
*/
private double calculateRouteDistanceWithAssociatedPickup(JobInsertionContext context){
double routeDistance = 0;
int pos... | /contribs/freight/src/main/java/org/matsim/contrib/freight/jsprit/DistanceConstraint.java |
robustness-copilot_data_162 | /**
* Create AccessTokenAuthentication component for authenticating user represented by
* the given token.
* @param accessToken - User's Bearer token
* @return - this CallBuilder instance
*/
public CallBuilder withAuthentication(String accessToken){
if (!isNullOrEmpty(accessToken)) {
this.he... | /operator/src/main/java/oracle/kubernetes/operator/helpers/CallBuilder.java |
robustness-copilot_data_163 | /**
* This function finds rings and uses aromaticity detection code to
* aromatize the molecule.
* @param mol input molecule
*/
public static void aromatizeMolecule(IAtomContainer mol){
IRingSet ringSet = null;
try {
AllRingsFinder arf = new AllRingsFinder();
ringSet = arf.f... | /legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java |
robustness-copilot_data_164 | /**
* Creates a copy of {@code this}, with identical business logic fields.
* E.g., {@link #label} would be duplicated; {@link #version} will not.
*
* @return A copy of {@code this}, except for the DB-related data.
*/
public FileMetadata createCopy(){
FileMetadata fmd = new FileMetadata()... | /src/main/java/edu/harvard/iq/dataverse/FileMetadata.java |
robustness-copilot_data_165 | /**
* Checks if this service should react to or ignore this replication action.
*
* @param replicationAction The replication action that is initiating this flush request
* @param replicationOptions The replication options that is initiating this flush request
* @return true is this service shou... | /bundle/src/main/java/com/adobe/acs/commons/replication/dispatcher/impl/DispatcherFlushRulesImpl.java |
robustness-copilot_data_166 | /**
* True, if the AdductFormula 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 AdductFormula is searched for
* @return True, if... | /base/data/src/main/java/org/openscience/cdk/formula/AdductFormula.java |
robustness-copilot_data_167 | /**
* Calculates 11 directional and 6 non-directional WHIM descriptors for.
* the specified weighting scheme
*
* @param container Parameter is the atom container.
* @return An ArrayList containing the descriptors in the order described above.
*/
public DescriptorValue calculate(IAtomConta... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java |
robustness-copilot_data_168 | /**
* Is the {@code mapping} of the stereochemistry in the query preserved in
* the target.
*
* @param mapping permutation of the query vertices
* @return the stereo chemistry is value
*/
public boolean test(final int[] mapping){
// n.b. not true for unspecified queries e.g. [C@?H](*)... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java |
robustness-copilot_data_169 | /**
* Parses CXSMILES layer and set attributes for atoms and bonds on the provided molecule.
*
* @param title SMILES title field
* @param mol molecule
*/
private void parseMolCXSMILES(String title, IAtomContainer mol) throws InvalidSmilesException{
CxSmilesState cxstate;
int pos;
... | /storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java |
robustness-copilot_data_170 | /**
* Helper method, that can be used to compute start time of legs.
* (it is also used internally).
* It is provided here, because such an operation is mainly useful for routing,
* but it may be externalized in a "util" class...
* @param config TODO
*/
public stat... | /matsim/src/main/java/org/matsim/core/router/TripRouter.java |
robustness-copilot_data_171 | /**
* The parenthesis convention is used to show a quantity by which a formula is multiplied.
* For example: (C12H20O11)2 really means that a C24H40O22 unit.
*
* @param formula Formula to correct
* @return Formula with the correction
*/
private static String breakExtractor(String f... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_172 | /**
* Returns the "contents" field of a document based on a collection docid. The method is named to be consistent with
* Lucene's {@link IndexReader#document(int)}, contra Java's standard method naming conventions.
*
* @param reader index reader
* @param docid collection docid
* @return the "contents... | /src/main/java/io/anserini/index/IndexReaderUtils.java |
robustness-copilot_data_173 | /**
* Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped
* up into descriptors.
*
* @param mol the atoms and bonds that make up the molecular object
* @return the various ring-based descriptors generated
*/
public DescriptorValue calcu... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/SmallRingDescriptor.java |
robustness-copilot_data_174 | /**
* Does the layout for the next RingSystem that is connected to those parts of
* the molecule that have already been laid out. Finds the next ring with an
* unplaced ring atom and lays out this ring. Then lays out the ring substituents
* of this ring. Then moves and rotates the laid out ring to m... | /tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java |
robustness-copilot_data_175 | /**
* Constructs an empty rule (useful for testing).
*
* @return An "empty" rule.
*/
static ValidationRule empty(){
return new ValidationRule(Severity.ERROR, "empty", "failure message", (i) -> Fail.empty());
} | /modules/openapi-generator-core/src/main/java/org/openapitools/codegen/validation/ValidationRule.java |
robustness-copilot_data_176 | /**
* Reads a CSV file, converts it into a dataverse DataTable.
*
* @param stream a <code>BufferedInputStream</code>.
* @return an <code>TabularDataIngest</code> object
* @throws java.io.IOException if a reading error occurs.
*/
public TabularDataIngest read(BufferedInputStream stream, Fi... | /src/main/java/edu/harvard/iq/dataverse/ingest/tabulardata/impl/plugins/csv/CSVFileReader.java |
robustness-copilot_data_177 | /**
* Replaces the special characters in the URLEncoded string with the replacement values defined by the spec.
*
* Partially copied from https://github.com/aws/aws-sdk-java: com.amazonaws.util.SdkHttpUtils (2017-05-19)
*
* @param string the string to replace characters in
* @param r... | /src/main/java/com/twilio/jwt/validation/RequestCanonicalizer.java |
robustness-copilot_data_178 | /**
* Return true if the subject is root or has the special ExemptFromNamespaceChecks principal.
*
* @param subject The identity of the user.
* @return if the user is except from namespace checks.
* @see #isRoot(javax.security.auth.Subject)
*/
public static boolean isExemptFromNamespaceCh... | /modules/common/src/main/java/org/dcache/auth/Subjects.java |
robustness-copilot_data_179 | /**
* Method called to get rid of candidate properties that are marked
* as ignored.
*/
protected void _removeUnwantedProperties(Map<String, POJOPropertyBuilder> props){
Iterator<POJOPropertyBuilder> it = props.values().iterator();
while (it.hasNext()) {
POJOPropertyBuilder prop = it.nex... | /src/main/java/com/fasterxml/jackson/databind/introspect/POJOPropertiesCollector.java |
robustness-copilot_data_180 | /**
* Returns a selection for all records that match neither of the given functions. In other words,
* if either (or both) of sel1 or sel2 is {@code true}, the record as a whole is {@code false}.
*/
public static Function<Table, Selection> neither(Function<Table, Selection> sel1, Function<Table, Selection> se... | /core/src/main/java/tech/tablesaw/api/QuerySupport.java |
robustness-copilot_data_181 | /**
* Converts the 'skills' attribute to a list of strings.
*
* @param attributes the {@link Attributes} container that is checked for the
* skill(s) to be converted.
* @return the {@link List} of skills, possibly empty, as parsed from the
* ... | /contribs/freight/src/main/java/org/matsim/contrib/freight/utils/FreightUtils.java |
robustness-copilot_data_182 | /**
* Sends the managed entity's properties to the client, if the client's snapshot is stale.
*
* @param session the client's session
*/
public void sendMessages(GlowSession session){
if (!needsUpdate) {
return;
}
int id = entity.entityId;
if (entity instanceof GlowPlayer) {... | /src/main/java/net/glowstone/entity/AttributeManager.java |
robustness-copilot_data_183 | /**
* Create a library entry from a SMILES string with the coordinates suffixed in binary. The
* entry should be created with {@link #encodeEntry(java.util.Map.Entry)} and not created
* manually. Note, the entry is not added to the library.
*
* @param str input string
* @return library ent... | /tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java |
robustness-copilot_data_184 | /**
* Calculate new point X in a B-A(-D)-C system. It forms a B-A(-D)(-C)-X
* system. (3) 3 ligands(B, C, D) of refAtom A (i) 1 points required; if A, B,
* C, D coplanar, no points. else vector is resultant of BA, CA, DA
*
*@param aPoint to which substituents are added
*@param bPoint... | /tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java |
robustness-copilot_data_185 | /**
* Determines if the ensure definition is the same as the the same-named oak:index definition.
*
* @param ensureDefinition the ensure index definition
* @param oakIndex the oak index definition
* @return true if the ensure definition and the oak index definition are different
* ... | /bundle/src/main/java/com/adobe/acs/commons/oak/impl/EnsureOakIndexJobHandler.java |
robustness-copilot_data_186 | /**
* The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili
* It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
* For this method will be only possible if the heavy atom has single bond.
*
*@param a... | /descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java |
robustness-copilot_data_187 | /**
* Check if given number is greater or equal to start range and minor or equal to end range.
*
* @param fieldValue - to be validated
* @throws IllegalArgumentException - if not in range
*/
protected void isInRange(final FieldValue<?> fieldValue){
if (fieldValue instanceof IntegerFieldVa... | /src/main/java/com/cronutils/model/field/expression/visitor/ValidationFieldExpressionVisitor.java |
robustness-copilot_data_188 | /**
* Verify that for every vertex adjacent to n, there should be at least one
* feasible candidate adjacent which can be mapped. If no such candidate
* exists the mapping of n -> m is not longer valid.
*
* @param n query vertex
* @param m target vertex
* @return mapping is still vali... | /base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java |
robustness-copilot_data_189 | /**
* Obtain the field name from a potential SD data header. If the header
* does not contain a field name, then null is returned. The method does
* not currently return field numbers (e.g. DT<n>).
*
* @param line an input line
* @return the field name
*/
static String dataHead... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java |
robustness-copilot_data_190 | /**
* From a provided set of cycles find the 5/6 member cycles that fit the MMFF aromaticity
* definition - {@link #isAromaticRing(int[], int[], int[], boolean[])}. The cycles of size 6
* are listed first.
*
* @param cycles initial set of cycles from
* @param contribution vector of p... | /tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAromaticTypeMapping.java |
robustness-copilot_data_191 | /**
* Adds a mapping between the reactant and product side to this
* Reaction.
*
* @param mapping Mapping to add.
* @see #mappings
*/
public void addMapping(IMapping mapping){
if (mappingCount + 1 >= map.length)
growMappingArray();
map[mappingCount] = mapping;
mappin... | /base/data/src/main/java/org/openscience/cdk/Reaction.java |
robustness-copilot_data_192 | /**
* Add a conformer to the end of the list.
*
* This method allows you to add a IAtomContainer object as another conformer.
* Before adding it ensures that the title of specific object matches the
* stored title for these conformers. It will also check that the number of
* atoms in the ... | /base/data/src/main/java/org/openscience/cdk/ConformerContainer.java |
robustness-copilot_data_193 | /**
* Removes the threshold of the given logger and appender combination in this threshold set. The
* new effective threshold will be derived from the regular inheritance rules.
*/
public synchronized void remove(LoggerName logger, String appender){
if (_rules.remove(logger, appender) != null) {
... | /modules/cells/src/main/java/dmg/util/logback/FilterThresholdSet.java |
robustness-copilot_data_194 | /**
* Sort the AtomContainers and multipliers using a provided Comparator.
* @param comparator defines the sorting method
*/
public void sortAtomContainers(final Comparator<IAtomContainer> comparator){
Integer[] indexes = new Integer[atomContainerCount];
for (int i = 0; i < indexes.length; i++) ... | /base/data/src/main/java/org/openscience/cdk/AtomContainerSet.java |
robustness-copilot_data_195 | /**
* Using the angular extents of vectors, determine the best position for a hydrogen label. The
* position with the most space is selected first. If multiple positions have the same amount of
* space, the one where the hydrogen position is most centred is selected. If all position are
* okay, the ... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java |
robustness-copilot_data_196 | /**
* Returns the Lucene {@link Document} based on a collection docid. The method is named to be consistent with Lucene's
* {@link IndexReader#document(int)}, contra Java's standard method naming conventions.
*
* @param reader index reader
* @param docid collection docid
* @return corresponding Lucene... | /src/main/java/io/anserini/index/IndexReaderUtils.java |
robustness-copilot_data_197 | /**
* Applies the given function to a byte subtag if it is present, converting it to boolean first.
*
* @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 readBoolean(@Non... | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_198 | /**
* Checks if the CharSequence contains only Unicode letters or digits.
*
* <p>{@code null} will return {@code false}. An empty CharSequence (length()=0) will return
* {@code false}.
*
* <pre>
* StringUtils.isAlphanumeric(null) = false
* StringUtils.isAlphanumeric("") = false
* String... | /core/src/main/java/tech/tablesaw/util/StringUtils.java |
robustness-copilot_data_199 | /**
* Removes nodes from the network that have no incoming or outgoing links attached to them.
*/
public void removeNodesWithoutLinks(){
List<Node> toBeRemoved = new ArrayList<>();
for (Node node : this.network.getNodes().values()) {
if ((node.getInLinks().size() == 0) && (node.getOut... | /matsim/src/main/java/org/matsim/core/network/algorithms/MultimodalNetworkCleaner.java |
robustness-copilot_data_200 | /**
* Execute all aggregate functions for the given slice setting values in the appropriate
* destination column.
*/
private void processAggregateFunctions(TableSlice slice){
for (String toColumn : query.getArgumentList().getAggregateFunctions().keySet()) {
FunctionCall<AggregateFunctions> functio... | /core/src/main/java/tech/tablesaw/analytic/AnalyticQueryEngine.java |
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