id stringlengths 25 27 | content stringlengths 190 15.4k | max_stars_repo_path stringlengths 31 217 |
|---|---|---|
robustness-copilot_data_801 | /**
* Builds functions that map the fields from source CronDefinition to target.
*
* @param from - source CronDefinition
* @param to - target CronDefinition
*/
private void buildMappings(final CronDefinition from, final CronDefinition to){
final Map<CronFieldName, FieldDefinition> source... | /src/main/java/com/cronutils/mapper/CronMapper.java |
robustness-copilot_data_802 | /**
* Does the atom at index {@code i} have priority over the atom at index
* {@code j} for the tetrahedral atom {@code focus}.
*
* @param focus tetrahedral centre (or -1 if double bond)
* @param i adjacent atom index
* @param j adjacent atom index
* @return whether atom i has... | /tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java |
robustness-copilot_data_803 | /**
* Find out if the PortImplementation 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 optiona... | /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_804 | /**
* Checks if each next {@link ILigand} is different from the previous
* one according to the {@link CIPLigandRule}. It assumes that the input
* is sorted based on that rule.
*
* @param ligands array of {@link ILigand} to check
* @return true, if all ligands are different
*/
public... | /descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java |
robustness-copilot_data_805 | /**
* Builder for molecules (rather, for atom containers) from signature
* strings.
*
* @param signatureString the signature string to use
* @param coBuilder {@link IChemObjectBuilder} to build the returned atom container from
* @return an atom container
*/
public static IAtomContain... | /descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeSignature.java |
robustness-copilot_data_806 | /** Returns a column of the same type containing the first {@code numRows} of this column. */
Column<T> first(final int numRows){
int newRowCount = Math.min(numRows, size());
return inRange(0, newRowCount);
} | /core/src/main/java/tech/tablesaw/columns/Column.java |
robustness-copilot_data_807 | /**
* Returns a StringColumn with the year and month 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 but your sourc... | /core/src/main/java/tech/tablesaw/columns/datetimes/DateTimeMapFunctions.java |
robustness-copilot_data_808 | /**
* Reports on the options that have been inserted into the MATSim {@link Config}
* via the command line.
*/
private void reportOptions(){
logger.info(String.format("Received %d positional command line arguments:", positionalArguments.size()));
logger.info(" " + String.join(" , ", positionalArguments... | /matsim/src/main/java/org/matsim/core/config/CommandLine.java |
robustness-copilot_data_809 | /**
* Returns a List for looping over all isotopes in this adduct formula.
*
* @return A List with the isotopes in this adduct formula
*/
private List<IIsotope> isotopesList(){
List<IIsotope> isotopes = new ArrayList<IIsotope>();
Iterator<IMolecularFormula> componentIterator = component... | /base/data/src/main/java/org/openscience/cdk/formula/AdductFormula.java |
robustness-copilot_data_810 | /**
* Splits this partition by taking the cell at cellIndex and making two
* new cells - the first with the singleton splitElement and the second
* with the rest of the elements from that cell.
*
* @param cellIndex the index of the cell to split on
* @param splitElement the element to put ... | /tool/group/src/main/java/org/openscience/cdk/group/Partition.java |
robustness-copilot_data_811 | /**
* Increases the priority (=decrease the given double value) of the element.
* If the element ins not part of the queue, it is added. If the new priority
* is lower than the existing one, the method returns <tt>false</tt>
*
* @return <tt>true</tt> if the elements priority... | /matsim/src/main/java/org/matsim/core/router/priorityqueue/BinaryMinHeap.java |
robustness-copilot_data_812 | /**
* Layout the molecule, starts with ring systems and than aliphatic chains.
*
*@param ringSetMolecule ringSystems of the molecule
*/
private void layoutMolecule(List ringSetMolecule, IAtomContainer molecule, AtomPlacer3D ap3d, AtomTetrahedralLigandPlacer3D atlp3d, AtomPlacer atomPlacer) throws... | /tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java |
robustness-copilot_data_813 | /**
* Given a new proposed label or directoryLabel for a file, check against
* existing files if a duplicate directoryLabel/label combination would be
* created.
*/
public static boolean conflictsWithExistingFilenames(String pathPlusFilename, List<FileMetadata> fileMetadatas){
List<String> file... | /src/main/java/edu/harvard/iq/dataverse/ingest/IngestUtil.java |
robustness-copilot_data_814 | /**
* Applies the given function to a list subtag if it is present and its contents are double
* 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 readDoub... | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_815 | /**
* Position the mass label relative to the element label. The mass adjunct is position to the
* top left of the element label.
*
* @param massLabel mass label outline
* @param elementLabel element label outline
* @return positioned mass label
*/
TextOutline positionMassLabel(Te... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java |
robustness-copilot_data_816 | /**
* Searches for the current sling:resourceType under /content and replaces any nodes it finds
* with the newResourceType.
*
* @param oldResourceType The current sling:resourceType.
* @param newResourceType The new sling:resourceType to be used.
*/
protected final void searchAndUpdateRe... | /bundle/src/main/java/com/adobe/acs/commons/ondeploy/scripts/OnDeployScriptBase.java |
robustness-copilot_data_817 | /**
* Returns the "raw" field of a document based on an internal Lucene docid.
* The method is named to be consistent with Lucene's {@link IndexReader#document(int)}, contra Java's standard
* method naming conventions.
*
* @param ldocid internal Lucene docid
* @return the "raw" field the d... | /src/main/java/io/anserini/search/SimpleImpactSearcher.java |
robustness-copilot_data_818 | /**
* Checks to see if this tag is a strict, deep submap of the given CompoundTag.
*
* @param other The CompoundTag that should contain our values.
*/
public boolean matches(CompoundTag other){
for (Entry<String, Tag> entry : value.entrySet()) {
if (!other.value.containsKey(entry.getKey... | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_819 | /**
* Mass number for a atom with a given atomic number and exact mass.
*
* @param atomicNumber atomic number
* @param exactMass exact mass
* @return the mass number (or null) if no mass number was found
* @throws IOException isotope configuration could not be loaded
*/
private In... | /tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java |
robustness-copilot_data_820 | /**
* Checks whether this query atom matches a target atom.
*
* Currently a query pharmacophore atom will match a target pharmacophore group if the
* symbols of the two groups match. This is based on the assumption that
* pharmacophore groups with the same symbol will have the same SMARTS
... | /tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryAtom.java |
robustness-copilot_data_821 | /**
* For each item in the column, returns the same number with the sign changed. For example: -1.3
* returns 1.3, 2.135 returns -2.135 0 returns 0
*/
DoubleColumn neg(){
DoubleColumn newColumn = DoubleColumn.create(name() + "[neg]", size());
for (int i = 0; i < size(); i++) {
newColumn.set(i,... | /core/src/main/java/tech/tablesaw/columns/numbers/NumberMapFunctions.java |
robustness-copilot_data_822 | /**
* Copy all shipments from the existing carrier to the new carrier with
* shipments.
*
* @param carrierWS the "new" carrier with Shipments
* @param carrier the already existing carrier
*/
private static void copyShipments(Carrier carrierWS, Carrier carrier){
for (CarrierShipment carrierShipment : ... | /contribs/freight/src/main/java/org/matsim/contrib/freight/utils/FreightUtils.java |
robustness-copilot_data_823 | /**
* Convert a Java 2D shape to a list of points.
*
* @param shape a shape
* @return list of point
*/
static List<Point2D> pointsOf(final Shape shape){
final List<Point2D> points = new ArrayList<Point2D>();
final double[] coordinates = new double[6];
for (PathIterator i = shape.ge... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ConvexHull.java |
robustness-copilot_data_824 | /**
* Calculate the count of atoms of the largest pi system in the supplied {@link IAtomContainer}.
*
* <p>The method require one parameter:
* <ol>
* <li>if checkAromaticity is true, the method check the aromaticity,
* <li>if false, means that the aromaticity has already been checked
... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java |
robustness-copilot_data_825 | /**
* See if any of the provided filter patterns match the current path. TRUE, if no filters are received.
*
* @param filters An array of string making up the regex to match with the path. They should never
* be empty since there is a DEFAULT value.
* @param path The path to in... | /bundle/src/main/java/com/adobe/acs/commons/replication/dispatcher/impl/RefetchFlushContentBuilderImpl.java |
robustness-copilot_data_826 | /**
* Abort call when a label could not be parsed. The tokens are cleared
* and replaced with the original label.
*
* @param label the original label
* @param tokens the current tokens
* @return always returns false
*/
private static boolean failParse(String label, List<String> toke... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java |
robustness-copilot_data_827 | /**
* Returns the computed digest or null if overlapping writes have been detected.
*
* @return Checksum
*/
private Set<Checksum> finalizeChecksums(){
_ioStateWriteLock.lock();
try {
_isWritable = false;
} finally {
_ioStateWriteLock.unlock();
}
synchronized (_da... | /modules/dcache/src/main/java/org/dcache/pool/movers/ChecksumChannel.java |
robustness-copilot_data_828 | /**
* Method that can be used to serialize any Java value as
* a String. Functionally equivalent to calling
* {@link #writeValue(Writer,Object)} with {@link java.io.StringWriter}
* and constructing String, but more efficient.
*<p>
* Note: prior to version 2.1, throws clause included {@link... | /src/main/java/com/fasterxml/jackson/databind/ObjectMapper.java |
robustness-copilot_data_829 | /** Returns the base 10 log of the values in this column as a NumberColumn. */
DoubleColumn log10(){
DoubleColumn newColumn = DoubleColumn.create(name() + "[log10]", size());
for (int i = 0; i < size(); i++) {
newColumn.set(i, Math.log10(getDouble(i)));
}
return newColumn;
} | /core/src/main/java/tech/tablesaw/columns/numbers/NumberMapFunctions.java |
robustness-copilot_data_830 | /**
* Writes a IChemObject to the MDL RXN file formated output.
* It can only output ChemObjects of type Reaction
*
* @param object class must be of type Molecule or MoleculeSet.
*
* @see org.openscience.cdk.ChemFile
*/
public void write(IChemObject object) throws CDKException{
i... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNWriter.java |
robustness-copilot_data_831 | /**
* Iterates through array items and replaces any placeholders found.
*
* @param node Array node
* @param contentVariableReplacements current map of content variables
*/
private void replaceInArray(JsonNode node, Map<String, Object> contentVariableReplacements){
if (node.get(0) != null &... | /bundle/src/main/java/com/adobe/acs/commons/ccvar/filter/ContentVariableJsonFilter.java |
robustness-copilot_data_832 | /**
* if md5 is not the same as the original, then update lcoal cache.
* @param group ConfigGroupEnum
* @param <T> the type of class
* @param data the new config data
*/
protected void updateCache(final ConfigGroupEnum group, final List<T> data){
String json = GsonUtils.getInstance().toJso... | /shenyu-admin/src/main/java/org/apache/shenyu/admin/listener/AbstractDataChangedListener.java |
robustness-copilot_data_833 | /**
* Formats an int to fit into the connectiontable and changes it
* to a String.
*
* @param i The int to be formated
* @param l Length of the String
* @return The String to be written into the connectiontable
*/
private String formatMDLInt(int i, int l){
String s = ""... | /storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNWriter.java |
robustness-copilot_data_834 | /**
* Process atom labels from extended SMILES in a char iter.
*
* @param iter char iteration
* @param dest destination of labels (atomidx->label)
* @return parse success/failure
*/
private static boolean processAtomLabels(final CharIter iter, final Map<Integer, String> dest){
int ato... | /storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java |
robustness-copilot_data_835 | /**
* Method that will construct a POJONode and
* insert it at specified position in this array.
*
* @return This array node, to allow chaining
*/
public ArrayNode insertPOJO(int index, Object pojo){
return _insert(index, (pojo == null) ? nullNode() : pojoNode(pojo));
} | /src/main/java/com/fasterxml/jackson/databind/node/ArrayNode.java |
robustness-copilot_data_836 | /**
* Calculate new point(s) X in a B-A system to form B-A-X. Use C as reference
* for * staggering about the B-A bond (1a) 1 ligand(B) of refAtom (A) which
* itself has a ligand (C) (i) 1 points required; vector along AB vector (ii)
* 2 points: 2 vectors in ABC plane, staggered and eclipsed wrt... | /tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java |
robustness-copilot_data_837 | /**
* Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
* The first Atom end up in the origin, the second on on the x axis, and the third
* one in the XY plane. The rest is added by applying the Zmatrix distances, angles
* and dihedrals. Angles are in degrees.
*
... | /storage/io/src/main/java/org/openscience/cdk/geometry/ZMatrixTools.java |
robustness-copilot_data_838 | /**
* Adds or replaces a list subtag with a list of longs.
*
* @param key the key to write to
* @param list the list contents as longs, to convert to long tags
*/
public void putLongList(@NonNls String key, List<Long> list){
putList(key, TagType.LONG, list, LongTag::new);
} | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_839 | /**
* Get the collection of job statistics in the most recent week.
*
* @return collection of running task statistics data objects
*/
public List<JobRunningStatistics> findJobRunningStatisticsWeekly(){
if (!isRdbConfigured()) {
return Collections.emptyList();
}
return rdbReposi... | /elasticjob-cloud/elasticjob-cloud-scheduler/src/main/java/org/apache/shardingsphere/elasticjob/cloud/scheduler/statistics/StatisticManager.java |
robustness-copilot_data_840 | /**
* Evaluates the valence corrected chi index for a set of fragments.
*
* This method takes into account the S and P atom types described in
* Kier & Hall (1986), page 20 for which empirical delta V values are used.
*
* @param atomContainer The target <code>AtomContainer</code>
* @... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java |
robustness-copilot_data_841 | /**
* Associates the specified value with the specified coordinates in this
* QuadTree.
*
* @param x x-coordinate where the specified value is to be associated.
* @param y y-coordinate where the specified value is to be associated.
* @param value value to be associa... | /matsim/src/main/java/org/matsim/core/utils/collections/QuadTree.java |
robustness-copilot_data_842 | /**
* Clones this <code>Mapping</code> and the mapped <code>IChemObject</code>s.
*
* @return The cloned object
*/
public Object clone() throws CloneNotSupportedException{
Mapping clone = (Mapping) super.clone();
if (relation != null) {
clone.relation = new IChemObject[relation.leng... | /base/silent/src/main/java/org/openscience/cdk/silent/Mapping.java |
robustness-copilot_data_843 | /**
* Adds rows to destination for each row in table1 with the columns from table2 added as missing
* values.
*/
private void withMissingLeftJoin(Table destination, Table table1, Selection table1Rows, Set<Integer> ignoreColumns, boolean keepTable2JoinKeyColumns){
for (int c = 0; c < destination.columnCoun... | /core/src/main/java/tech/tablesaw/joining/DataFrameJoiner.java |
robustness-copilot_data_844 | /**
* Checks whether {@code this} dataset is locked for a given reason.
* @param reason the reason we test for.
* @return {@code true} iff the data set is locked for {@code reason}.
*/
public boolean isLockedFor(DatasetLock.Reason reason){
for (DatasetLock l : getLocks()) {
if (l.getRea... | /src/main/java/edu/harvard/iq/dataverse/Dataset.java |
robustness-copilot_data_845 | /**
* Clones this SingleElectron object, including a clone of the atom for which the
* SingleElectron is defined.
*
* @return The cloned object
*/
public Object clone() throws CloneNotSupportedException{
SingleElectron clone = (SingleElectron) super.clone();
if (atom != null) {
... | /base/data/src/main/java/org/openscience/cdk/SingleElectron.java |
robustness-copilot_data_846 | /**
* Evaluates the empirical delt V for some S environments.
*
* The method checks to see whether a S atom is in a -S-S-,
* -SO-, -SO2- group and returns the empirical values noted
* in Kier & Hall (1986), page 20.
*
* @param atom The S atom in question
* @param atomCo... | /descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java |
robustness-copilot_data_847 | /**
* Check if the admin protocol channel is using a secure protocol like T3S or HTTPS.
* @return true is a secure protocol is being used
*/
public boolean isLocalAdminProtocolChannelSecure(){
boolean adminProtocolPortSecure = false;
boolean adminProtocolPortFound = false;
if (networkAccessPoints ... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsServerConfig.java |
robustness-copilot_data_848 | /**
* When a job is submitted, it adds itself as the child of a parent job. When it terminates, it
* removes itself from the parent list. The multimap implementation automatically removes the
* parent key from the table when its child collection is empty.
* <p>
* Breadth-first directories do ... | /modules/dcache-bulk/src/main/java/org/dcache/services/bulk/handlers/BulkJobCompletionHandler.java |
robustness-copilot_data_849 | /**
* Create the port and attach it to the process.
*
* @param userId the name of the calling user
* @param port the port values
* @param entityTpeName the type name
* @param externalSourceName the unique name of the external source
* @param processGUID ... | /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_850 | /**
* Parse a {@link JsonNode} and produce the corresponding {@link NodeWriter}.
*
* @param node the {@link JsonNode} to parse.
* @return a {@link NodeWriter} corresponding to the given JSON node
* @throws JsonPatternException denotes an invalid pattern
*/
private NodeWriter<Event> parse... | /src/main/java/net/logstash/logback/pattern/AbstractJsonPatternParser.java |
robustness-copilot_data_851 | /**
* Creates a new sumo handler by reading data from xml file.
*/
static SumoNetworkHandler read(File file) throws ParserConfigurationException, SAXException, IOException{
SAXParserFactory factory = SAXParserFactory.newInstance();
SAXParser saxParser = factory.newSAXParser();
SumoNetworkHandler... | /contribs/sumo/src/main/java/org/matsim/contrib/sumo/SumoNetworkHandler.java |
robustness-copilot_data_852 | /**
* Parse a string of namespace names and return them as a collection.
* @param namespaceString a comma-separated list of namespace names
* @return Namespace list
*/
public static Collection<String> parseNamespaceList(String namespaceString){
Collection<String> namespaces = Stream.of(namespaceString.... | /operator/src/main/java/oracle/kubernetes/operator/helpers/NamespaceHelper.java |
robustness-copilot_data_853 | /**
* Receive a binary encoded 'picture' message from the socket (or actor).
* This method is similar to {@link org.zeromq.ZMQ.Socket#recv()}, except the arguments are encoded
* in a binary format that is compatible with zproto, and is designed to
* reduce memory allocations.
*
* @param pi... | /src/main/java/org/zeromq/proto/ZPicture.java |
robustness-copilot_data_854 | /** Returns a column of the same type containing the last {@code numRows} of this column. */
Column<T> last(final int numRows){
int newRowCount = Math.min(numRows, size());
return inRange(size() - newRowCount, size());
} | /core/src/main/java/tech/tablesaw/columns/Column.java |
robustness-copilot_data_855 | /**
* Iterates over keys to replace any placeholders in the values.
*
* @param node Object node
* @param contentVariableReplacements current map of content variables
*/
private void replaceInObject(JsonNode node, Map<String, Object> contentVariableReplacements){
Iterator<String> fieldNames... | /bundle/src/main/java/com/adobe/acs/commons/ccvar/filter/ContentVariableJsonFilter.java |
robustness-copilot_data_856 | /**
* Non destructively split a molecule into two parts at the specified bond.
*
* Note that if a ring bond is specified, the resultant list will contain
* teh opened ring twice.
*
* @param atomContainer The molecule to split
* @param bond The bond to split at
* @return A list co... | /tool/fragment/src/main/java/org/openscience/cdk/fragment/FragmentUtils.java |
robustness-copilot_data_857 | /**
* This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
* Added by Asad since CDK one doesn't pick up the correct changes
* @param list The list produced by the getMap method.
* @param sourceGraph first molecule. Mu... | /legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java |
robustness-copilot_data_858 | /**
* Return true if the SqlStatement class queries the database in any way to determine Statements to execute.
* If the statement queries the database, it cannot be used in updateSql type operations
*/
public boolean generateStatementsVolatile(SqlStatement statement, Database database){
for (SqlGen... | /liquibase-core/src/main/java/liquibase/sqlgenerator/SqlGeneratorFactory.java |
robustness-copilot_data_859 | /**
* Determines if, according to the algorithms implemented in this class, the given
* AtomContainer has properly distributed double bonds.
*
* @param m {@link IAtomContainer} to check the bond orders for.
* @return true, if bond orders are properly distributed
* @throws CDKException thr... | /legacy/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java |
robustness-copilot_data_860 | /**
* Adds a new column to the column list of this PrimaryKey. The first column has the position 0.
* If you specify a position that is greater than the number of columns present, undefined
* columns (NULL expressions) will be added as padding. If a position that is already
* occupied by a column is... | /liquibase-core/src/main/java/liquibase/structure/core/PrimaryKey.java |
robustness-copilot_data_861 | /**
* Repeat a String {@code repeat} times to form a new String.
*
* <pre>
* StringUtils.repeat(null, 2) = null
* StringUtils.repeat("", 0) = ""
* StringUtils.repeat("", 2) = ""
* StringUtils.repeat("a", 3) = "aaa"
* StringUtils.repeat("ab", 2) = "abab"
* StringUtils.repeat("a", -2) = ""... | /core/src/main/java/tech/tablesaw/util/StringUtils.java |
robustness-copilot_data_862 | /**
* Calculates the cheapest route from Node 'fromNode' to Node 'toNode' at
* starting time 'startTime'.
*
* @param fromNode
* The Node at which the route should start.
* @param toNode
* The Node at which the route should end.
... | /matsim/src/main/java/org/matsim/core/router/Dijkstra.java |
robustness-copilot_data_863 | /**
* Create a stereo encoder for all potential 2D and 3D double bond stereo
* configurations.
*
* @param container an atom container
* @param graph adjacency list representation of the container
* @return a new encoder for tetrahedral elements
*/
public StereoEncoder create(IAto... | /tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java |
robustness-copilot_data_864 | /**
* Returns {@code this}' string representation. Differs from {@link #toString}
* which can also contain debug data, if needed.
*
* @return The string representation of this global id.
*/
public String asString(){
if (protocol == null || authority == null || identifier == null) {
... | /src/main/java/edu/harvard/iq/dataverse/GlobalId.java |
robustness-copilot_data_865 | /**
* Assigns a set of rings to groups each sharing a bond.
*
* @param rBondsArray
* @return A List of Lists each containing the ring indices of a set of fused rings
*/
private List<List<Integer>> assignRingGroups(List<Integer[]> rBondsArray){
List<List<Integer>> ringGroups;
ringGroups... | /legacy/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java |
robustness-copilot_data_866 | /**
* Access the default position of the hydrogen label when the atom has no
* bonds.
*
* @param atom hydrogens will be labelled
* @return the position
*/
static HydrogenPosition usingDefaultPlacement(final IAtom atom){
if (PREFIXED_H.contains(Elements.ofNumber(atom.getAtomicNumber()... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java |
robustness-copilot_data_867 | /**
* Creates a WLSServerConfig object using an "servers" or "serverTemplates" item parsed from JSON
* result from WLS REST call.
*
* @param serverConfigMap A Map containing the parsed "servers" or "serverTemplates" element for a
* WLS server or WLS server template.
* @return A new WlsServerConfig... | /operator/src/main/java/oracle/kubernetes/operator/wlsconfig/WlsServerConfig.java |
robustness-copilot_data_868 | /**
* Creates a schema generator, suitably customized for generating Kubernetes CRD schemas.
*/
public static SchemaGenerator createCrdSchemaGenerator(){
SchemaGenerator generator = new SchemaGenerator();
generator.defineAdditionalProperties(Quantity.class, "string");
generator.setForbidAdditionalPro... | /operator/src/main/java/oracle/kubernetes/weblogic/domain/model/CrdSchemaGenerator.java |
robustness-copilot_data_869 | /**
* Finds the end character index of the parameter within the paramsString that starts at startIndex.
*
* Takes into account nesting of parameters.
*
* @param paramsString
* @param startIndex index within paramsString to start looking
* @return index at which the parameter string en... | /src/main/java/net/logstash/logback/appender/WaitStrategyFactory.java |
robustness-copilot_data_870 | /**
* Returns the Elements ordered according to (approximate) probability of occurrence.
*
* <p>This begins with the "elements of life" C, H, O, N, (Si, P, S, F, Cl),
* then continues with the "common" chemical synthesis ingredients, closing off
* with the tail-end of the periodic table in atom... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java |
robustness-copilot_data_871 | /**
* Converts a given string into a Bayesian model instance, or throws an exception if it is not valid.
*
* @param str string containing the serialised model
* @return instantiated model that can be used for predictions
*/
public static Bayesian deserialise(String str) throws IOException{
... | /tool/model/src/main/java/org/openscience/cdk/fingerprint/model/Bayesian.java |
robustness-copilot_data_872 | /**
* Recycle the instance before returning it to the pool.
* Sub-classes may override this method if they wish to implement their own custom logic.
*
* @param instance the instance to recycle
* @return {@code true} if the instance can be recycled and returned to the pool, {@code false} if not... | /src/main/java/net/logstash/logback/util/ThreadLocalHolder.java |
robustness-copilot_data_873 | /**
* Renames any column header that appears more than once. Subsequent appearances have "-[count]"
* appended; For example, the first (or only) appearance of "foo" is named "foo", the second
* appearance is named "foo-2" The header array is modified in place.
*
* @param headerNames The header names to b... | /core/src/main/java/tech/tablesaw/io/FileReader.java |
robustness-copilot_data_874 | /**
* Partition the bonding partners of a given atom into placed (coordinates
* assinged) and not placed.
*
*@param atom The atom whose bonding partners are to be
* partitioned
*@param unplacedPartners A vector for the unplaced bonding partners to go in
*@param ... | /tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java |
robustness-copilot_data_875 | /**
* Constructs a new {@link IDifference} object.
*
* @param name a name reflecting the nature of the created {@link IDifference}
* @param first the first object to compare
* @param second the second object to compare
* @return an {@link IDifference} reflecting the differences be... | /misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/Point3dDifference.java |
robustness-copilot_data_876 | /**
* Creates a function to adjust the freespeed for urban links.
* @see LinkProperties#DEFAULT_FREESPEED_FACTOR
*
* @apiNote Can be used as example, but no public access currently
*/
static AfterLinkCreated adjustFreespeed(final double factor){
return (link, osmTags, direction) -> {
... | /contribs/osm/src/main/java/org/matsim/contrib/osm/networkReader/SupersonicOsmNetworkReader.java |
robustness-copilot_data_877 | /**
* Returns a one line string representation of this LonePair.
* This method is conform RFC #9.
*
* @return The string representation of this LonePair
*/
public String toString(){
StringBuffer resultString = new StringBuffer();
resultString.append("LonePair(");
resultString.ap... | /base/silent/src/main/java/org/openscience/cdk/silent/LonePair.java |
robustness-copilot_data_878 | /**
* Parse a JSON pattern and produce the corresponding {@link NodeWriter}.
* Returns <em>null</em> if the pattern is invalid, null or empty. An error status is
* logged when the pattern is invalid and parsing failed.
*
* @param pattern the JSON pattern to parse
* @return a {@link NodeWr... | /src/main/java/net/logstash/logback/pattern/AbstractJsonPatternParser.java |
robustness-copilot_data_879 | /**
* Adds or replaces a list subtag, converting the list entries to tags.
*
* @param <V> the list elements' Java type
* @param key the key to write to
* @param type the list elements' tag type
* @param value the list contents, as objects to convert to tags
* @param tagCreator a funct... | /src/main/java/net/glowstone/util/nbt/CompoundTag.java |
robustness-copilot_data_880 | /**
* Locate a stereo bond adjacent to the {@code atom}.
*
* @param atom an atom
* @return a stereo bond or null if non found
*/
private StereoBond findStereoBond(IAtom atom){
for (IBond bond : stereoBonds) if (bond.contains(atom))
return (StereoBond) bond;
return null;
} | /legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java |
robustness-copilot_data_881 | /**
* Gateway method the Filter uses to determine if the request is a candidate for processing by Assets Folder Properties Support.
* These checks should be fast and fail broadest and fastest first.
*
* @param request the request
* @return true if Assets Folder Properties Support should process... | /bundle/src/main/java/com/adobe/acs/commons/dam/impl/AssetsFolderPropertiesSupport.java |
robustness-copilot_data_882 | /**
* Generate a SMARTS for the substructure formed of the provided
* atoms.
*
* @param atomIdxs atom indexes
* @return SMARTS, null if an empty array is passed
*/
public String generate(int[] atomIdxs){
if (atomIdxs == null)
throw new NullPointerException("No atom indexes pro... | /tool/smarts/src/main/java/org/openscience/cdk/smarts/SmartsFragmentExtractor.java |
robustness-copilot_data_883 | /**
* Adds all rings of another RingSet if they are not already part of this ring set.
*
* If you want to add a single ring to the set use {@link #addAtomContainer(org.openscience.cdk.interfaces.IAtomContainer)}
*
* @param ringSet the ring set to be united with this one.
*/
public void... | /base/silent/src/main/java/org/openscience/cdk/silent/RingSet.java |
robustness-copilot_data_884 | /**
* Initialise our expiry time to some point in the future.
*
* @param lifetime the time, in seconds.
*/
private void becomeMortal(long lifetime){
_whenIShouldExpire = new Date(System.currentTimeMillis() + TimeUnit.SECONDS.toMillis(lifetime));
} | /modules/dcache-info/src/main/java/org/dcache/services/info/base/StateComposite.java |
robustness-copilot_data_885 | /**
* Iterate over the underlying rows in the source table. If you set one of the rows while
* iterating it will change the row in the source table.
*/
public Iterator<Row> iterator(){
return new Iterator<Row>() {
private final Row row = new Row(TableSlice.this);
@Override
public... | /core/src/main/java/tech/tablesaw/table/TableSlice.java |
robustness-copilot_data_886 | /**
* Capitalizes a String changing the first character to title case as per {@link
* Character#toTitleCase(int)}. No other characters are changed.
*
* <p>A {@code null} input String returns {@code null}.
*
* <pre>
* StringUtils.capitalize(null) = null
* StringUtils.capitalize("") = ""
* ... | /core/src/main/java/tech/tablesaw/util/StringUtils.java |
robustness-copilot_data_887 | /**
* Access the bounds of a shape that have been transformed.
*
* @param shape any shape
* @return the bounds of the shape transformed
*/
private Rectangle2D transformedBounds(Shape shape){
Rectangle2D rectangle2D = shape.getBounds2D();
Point2D minPoint = new Point2D.Double(rectangle2... | /display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/TextOutline.java |
robustness-copilot_data_888 | /**
* Actual conversion implementation: instead of using existing read
* and write methods, much of code is inlined. Reason for this is
* that we must avoid root value wrapping/unwrapping both for efficiency and
* for correctness. If root value wrapping/unwrapping is actually desired,
* caller ... | /src/main/java/com/fasterxml/jackson/databind/ObjectMapper.java |
robustness-copilot_data_889 | /**
* In the minimal IMolecularFormula must contain all those IElement found in the
* minimal IMolecularFormula.
*
* @param formulaMax A IMolecularFormula which contains the maximal representation of the Elements
* @param formulaMin A IMolecularFormula which contains the minimal representatio... | /tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java |
robustness-copilot_data_890 | /**
* Collect and return a report row for the workflow status. Method is package scope for unit tests.
* @param status the status to report upon.
* @return the row of data
*/
EnumMap<ReportColumns, Object> report(WorkflowRemovalStatus status){
final EnumMap<ReportColumns, Object> row = new En... | /bundle/src/main/java/com/adobe/acs/commons/mcp/impl/processes/WorkflowRemover.java |
robustness-copilot_data_891 | /**
* Creates a default configuration properties with some common values like: application.tmpdir,
* application.charset and pid (process ID).
*
* @return A configuration object.
*/
public static Config defaults(){
Path tmpdir = Paths.get(System.getProperty("user.dir"), "tmp");
Map<String, Strin... | /jooby/src/main/java/io/jooby/Environment.java |
robustness-copilot_data_892 | /**
* Removes rings which do not have all sp2/planar3 aromatic atoms.
* and also gets rid of rings that have more than 8 atoms in them.
*
* @param m The {@link IAtomContainer} from which we want to remove rings
* @return The set of reduced rings
*/
private IRingSet removeExtraRings(IAtomC... | /legacy/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java |
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