DGWSProxy

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com.discoverygate.webservice
Class DGWSProxy

java.lang.Object
  com.discoverygate.webservice.DGWSProxy

All Implemented Interfaces:: DGWS, java.rmi.Remote

public class DGWSProxy
extends java.lang.Object
implements DGWS
extends java.lang.Object
implements DGWS

Constructor Summary
`DGWSProxy()`
`DGWSProxy(java.lang.String endpoint)`

Method Summary
`void`	`closeStatefulQuery(ServiceRequest arg0)` Terminates the stateful query specified by the statefulQueryKey in the ServiceRequest object.
`java.lang.String[]`	`convertStructureToMolfile(ServiceRequest arg0, java.lang.String[] arg1)` Returns the array of molecules as an array of molfiles (or the array of reactions as an array of rxnfiles).
`ExistenceResult[]`	`findSourceMolecule(ServiceRequest arg0, Datasource arg1, ExistenceRequest[] arg2)` Determines whether the molecules specified in the `com.discoverygate.webservice.types.com.discoverygate.webservice.types.ExistenceRequest` array exist in the source database.
`CatalogResults`	`getCatalogsById(ServiceRequest arg0, CatalogId[] arg1)` Returns a CatalogsResults object (a list of Catalog objects) for a given list of Catalogs IDs.
`XMLResults`	`getCatalogsByIdXML(ServiceRequest arg0, CatalogId[] arg1)` Identical to the `com.discoverygate.webservice.types.com.discoverygate.webservice.types.getCatalogsById` method except that the results are returned in XML format.
`ClassificationVocabulary`	`getClassificationVocabulary(ServiceRequest arg0, VocabularyVersion arg1)` Returns the Classification vocabulary if the VocabularyVersion passed is not equal to the current server version.
`java.lang.String`	`getClassificationVocabularyXML(ServiceRequest arg0, VocabularyVersion arg1)` Same as getClassificationVocabulary except that the vocabulary is returned as a string of XML.
`DGWS`	`getDGWS()`
`java.lang.String`	`getEndpoint()`
`MoleculeResults`	`getMoleculesByCatalogId(ServiceRequest arg0, CatalogId arg1, BulkFineType arg2)` Returns the source molecules for a given CatalogId.
`XMLResults`	`getMoleculesByCatalogIdXML(ServiceRequest arg0, CatalogId arg1, BulkFineType arg2)` Same as getMoleculesByCatalogId except that the results are returned in XML format.
`Molecule`	`getMoleculesByCatalogItem(ServiceRequest arg0, CatalogItem[] arg1)` Returns a set of source molecules for the catalog items specified by the catalog numbers.
`java.lang.String`	`getMoleculesByCatalogItemXML(ServiceRequest arg0, CatalogItem[] arg1)` Same as `getMoleculesByCatalogItem` method except that the molecule container is returned as a string of XML.
`MoleculeResults`	`getMoleculesByCatalogNumbers(ServiceRequest arg0, java.lang.String[] arg1)` Returns the source molecules for a given CatalogIds.
`XMLResults`	`getMoleculesByCatalogNumbersXML(ServiceRequest arg0, java.lang.String[] arg1)` Same as getMoleculesByCatalogNumbers except that the results are returned in XML format.
`MoleculeResults`	`getMoleculesByClassification(ServiceRequest arg0, MoleculeSearch[] arg1, java.lang.String arg2)` Returns the molecules that are classified by the class-type passed and optionally conform to the structure search specified by the parameter `aCriteria`.
`XMLResults`	`getMoleculesByClassificationXML(ServiceRequest arg0, MoleculeSearch[] arg1, java.lang.String arg2)` Same as getMoleculesByClassification except that the results are returned in XML format.
`MoleculeResults`	`getMoleculesById(ServiceRequest arg0, MoleculeId[] arg1)` Returns an array of `Molecule` within a results container for the array of Molecule IDs.
`XMLResults`	`getMoleculesByIdXML(ServiceRequest arg0, MoleculeId[] arg1)` Identical to the `com.discoverygate.webservice.types.getMoleculesById` method except that the results returned are in XML format.
`MoleculeResults`	`getMoleculesByNames(ServiceRequest arg0, java.lang.String[] arg1)` Returns an array of `Molecule entities within a results container for the specified wildcard.`
`XMLResults`	`getMoleculesByNamesXML(ServiceRequest arg0, java.lang.String[] arg1)` Identical to the `com.discoverygate.webservice.types.getMoleculesByName` method except that the results returned are in XML format.
`MoleculeResults`	`getMoleculesByQuery(ServiceRequest arg0, MoleculeSearch[] arg1, java.lang.String arg2)` For internal use only - do not use this in your application.
`XMLResults`	`getMoleculesByQueryXML(ServiceRequest arg0, MoleculeSearch[] arg1, java.lang.String arg2)` For internal use only - do not use this in your application.
`MoleculeResults`	`getMoleculesBySourceId(ServiceRequest arg0, SourceId[] arg1)` Returns the top-level molecules that correspond to the list of SourceId objects.
`Molecule`	`getMoleculesBySourceIdMerged(ServiceRequest arg0, SourceId[] arg1)` Returns an unpopulated Molecule container that contains source molecule objects, as well as their hierarchies fetched with the retrieval flags.
`java.lang.String`	`getMoleculesBySourceIdMergedXML(ServiceRequest arg0, SourceId[] arg1)` This method is the same as getMoleculeMergedBySourceId except that it returns the result as a single XML string.
`XMLResults`	`getMoleculesBySourceIdXML(ServiceRequest arg0, SourceId[] arg1)` Same as getMoleculesBySourceId except that the results are returned in XML format.
`MoleculeResults`	`getMoleculesByStructure(ServiceRequest arg0, MoleculeSearch[] arg1)` Returns an array of `Molecule` within a results container that satisfy the query specified by a combination of the boolean structure searches within the aCriteria parameter.
`XMLResults`	`getMoleculesByStructureXML(ServiceRequest arg0, MoleculeSearch[] arg1)` Identical to the `com.discoverygate.webservice.types.getMoleculesByStructure` except that the results returned are in XML format.
`AvailabilityFilterResults`	`getMoleculesFilterInfoById(ServiceRequest arg0, MoleculeId[] arg1)` Returns an array of AvailabilityFilter within a results container for the given array of Molecule IDs
`XMLResults`	`getMoleculesFilterInfoByIdXML(ServiceRequest arg0, MoleculeId[] arg1)` Identical to the `com.discoverygate.webservice.types.getMoleculesFilterInfoById` method except that the results returned are in XML format.
`SimilarityResult[]`	`getMoleculeSimilarity(ServiceRequest arg0, MoleculeId[] arg1, Structure arg2, SimilarityType arg3)` Returns the list of SimilarityResult (Molecule ID and similarity percentage) of the given IDs against the given structure, for the specified similarity type.
`MoleculeSourceResults`	`getMoleculeSourcesByMoleculeId(ServiceRequest arg0, Datasource arg1, MoleculeId[] arg2)` For a list of `com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeId`'s, determines which data sources contain the IDs.
`XMLResults`	`getMoleculeSourcesByMoleculeIdXML(ServiceRequest arg0, Datasource arg1, MoleculeId[] arg2)` Identical to the `com.discoverygate.webservice.types.com.discoverygate.webservice.types.getMoleculeSourcesByMoleculeId` method except that the results returned are in XML format.
`PatentResults`	`getPatentsByTitle(ServiceRequest arg0, java.lang.String arg1)` Returns the Patent entities (DGWS classes) that match the search criteria passed in the `aTextQuery` parameter.
`XMLResults`	`getPatentsByTitleXML(ServiceRequest arg0, java.lang.String arg1)` The same as getPatentsByTitle except that the response is returned in XML form.
`ProcurementVocabularies`	`getProcurementVocabulary(ServiceRequest arg0, VocabularyVersion arg1)` Returns the `ProcurementVocabularies` object if the VocabularyVersion passed is not equal to the current server version.
`java.lang.String`	`getProcurementVocabularyXML(ServiceRequest arg0, VocabularyVersion arg1)` Same as getProcurementVocabulary except that the vocabulary is returned as a string of XML.
`ProductResults`	`getProductsByMoleculeAndSuppliers(ServiceRequest arg0, SourceId[] arg1, SupplierId[] arg2)` Returns an array of `Product` within a results container for the given array of Molecule IDs and Supplier IDs.
`XMLResults`	`getProductsByMoleculeAndSuppliersXML(ServiceRequest arg0, SourceId[] arg1, SupplierId[] arg2)` Identical to the `com.discoverygate.webservice.types.getProductsByMoleculeandSuppliers` method except that the results returned are in XML format.
`RxnCitationResults`	`getReactionCitations(ServiceRequest arg0, CitationCriteria arg1)` Returns the Reaction citation entities (DGWS classes) that conform to the citation criteria passed to the method.
`XMLResults`	`getReactionCitationsXML(ServiceRequest arg0, CitationCriteria arg1)` Same as getReactionCitations except that the result are returned in XML format
`Classification[]`	`getReactionClassification(ServiceRequest arg0, Structure[] arg1)` Returns an object containing the Broad, Medium and Narrow InfoChem class-codes for each rxnfile given in the array.
`ReactionResults`	`getReactionsById(ServiceRequest arg0, ReactionId[] arg1)` Returns an array of `Reaction` within a results container for the array of Reaction IDs.
`XMLResults`	`getReactionsByIdXML(ServiceRequest arg0, ReactionId[] arg1)` Identical to the `getReactionsById` method except that the results returned are in XML format.
`ReactionResults`	`getReactionsByProduct(ServiceRequest arg0, MoleculeSearch[] arg1, RxnProductCriteria arg2)` Gets the reactions where at least one of the products conforms to the search created from the MoleculeSearch[] passed to the method.
`XMLResults`	`getReactionsByProductXML(ServiceRequest arg0, MoleculeSearch[] arg1, RxnProductCriteria arg2)` The same as getReactionsByProduct except that the response is returned in XML form.
`ReactionResults`	`getReactionsByQuery(ServiceRequest arg0, ReactionSearch[] arg1, java.lang.String arg2)` For internal use only - do not use this in your application.
`XMLResults`	`getReactionsByQueryXML(ServiceRequest arg0, ReactionSearch[] arg1, java.lang.String arg2)` For internal use only - do not use this in your application.
`ReactionResults`	`getReactionsByStructure(ServiceRequest arg0, ReactionSearch[] arg1)` Returns an array of `Reaction` within a results container that satisfy the query specified.
`XMLResults`	`getReactionsByStructureXML(ServiceRequest arg0, ReactionSearch[] arg1)` Identical to the `com.discoverygate.webservice.types.getReactionsByStructure` except that the results returned are in XML format.
`ReactionResults`	`getReactionsByVariation(ServiceRequest arg0, RxnVariationId[] arg1)` Identical to the `getReactionsById` method except that the VariationId is specified.
`XMLResults`	`getReactionsByVariationXML(ServiceRequest arg0, RxnVariationId[] arg1)` Identical to the `com.discoverygate.webservice.types.getReactionsByVariation` method except that the results returned are in XML format.
`ReactionFilterResults`	`getReactionsFilterInfoById(ServiceRequest arg0, ReactionId[] arg1)` Returns an array of `RxnFilterVariation` within a results container for the array of Reaction IDs.
`XMLResults`	`getReactionsFilterInfoByIdXML(ServiceRequest arg0, ReactionId[] arg1)` Identical to the `com.discoverygate.webservice.types.getReactionsFilterInfoById` method except that the results returned are in XML format.
`ReactionVocabulary`	`getReactionVocabulary(ServiceRequest arg0, VocabularyVersion arg1)` Returns the Reaction vocabulary if the VocabularyVersion passed is not equal to the current server version.
`java.lang.String`	`getReactionVocabularyXML(ServiceRequest arg0, VocabularyVersion arg1)` Same as getReactionVocabulary except that the vocabulary is returned as a string of XML.
`java.lang.String`	`getSchema(ServiceRequest arg0, SchemaType arg1)` Returns the Schema (XSD format) of the root-level object specified in the SchemaType.
`ServiceInformation`	`getServiceInformation(ServiceRequest arg0)` Returns information associated with the license, such as the version string of the service, a list of retrieval flags, a list of sources and their copyright strings.
`MoleculeResults`	`getSourceMoleculesByStructure(ServiceRequest arg0, MoleculeSearch[] arg1, Datasource arg2)` Searches the source database specified by the Datasource parameter for the MoleculeSearch criteria.
`XMLResults`	`getSourceMoleculesByStructureXML(ServiceRequest arg0, MoleculeSearch[] arg1, Datasource arg2)` Same as getSourceMoleculesByStructure except that the results are returned in XML format.
`SimilaritySourceResult[]`	`getSourceMoleculeSimilarity(ServiceRequest arg0, SourceId[] arg1, Structure arg2, SimilarityType arg3)` Operates in the same way as `getMoleculeSimilarity` except that the inputs and outputs are related to source molecule IDs.
`MoleculeSourceResults`	`getSourceSummaryByMoleculeId(ServiceRequest arg0, Datasource[] arg1, MoleculeId[] arg2)` Determines the for a list of `MoleculeId`'s in which data sources they exist.
`XMLResults`	`getSourceSummaryByMoleculeIdXML(ServiceRequest arg0, Datasource[] arg1, MoleculeId[] arg2)` Identical to the `com.discoverygate.webservice.types.getSourceSummaryByMoleculeId` method except that the results returned are in XML format.
`SupplierResults[]`	`getSuppliers(ServiceRequest arg0, java.lang.String arg1)` Returns an array of `com.discoverygate.webservice.types.Supplier` within a results container for the specified wildcard and procurement datasource.
`SupplierResults`	`getSuppliersById(ServiceRequest arg0, SupplierId[] arg1)` Returns a SupplierResults object (a list of Supplier objects) for a given list of Supplier IDs.
`XMLResults`	`getSuppliersByIdXML(ServiceRequest arg0, SupplierId[] arg1)` Identical to the `com.discoverygate.webservice.types.getSuppliersById` method except that the results are returned in XML format.
`XMLResults[]`	`getSuppliersXML(ServiceRequest arg0, java.lang.String arg1)` Identical to the `com.discoverygate.webservice.types.getSuppliers` method except that the results returned are in XML format.
`ExperimentResults`	`getToxicityExperiments(ServiceRequest arg0, MoleculeSearch[] arg1, ExperimentCriteria arg2)` Returns the toxicity experiments that conform to the experiment criteria passed, and optionally conform to the structure search specified by the parameter `aSearch`.
`XMLResults`	`getToxicityExperimentsXML(ServiceRequest arg0, MoleculeSearch[] arg1, ExperimentCriteria arg2)` Same as getToxicityExperiments except that the results are returned in XML format
`ToxPublication[]`	`getToxicityPublications(ServiceRequest arg0, ToxCoden[] arg1)` Returns a list of Toxicology publication objects for the Codens passed to the method.
`ToxicityVocabulary`	`getToxicityVocabulary(ServiceRequest arg0, VocabularyVersion arg1)` Returns the Toxicity vocabulary if the VocabularyVersion passed is not equal to the current server version.
`java.lang.String`	`getToxicityVocabularyXML(ServiceRequest arg0, VocabularyVersion arg1)` Same as getToxicityVocabulary except that the vocabulary is returned as a string of XML.
`XMLResults`	`runProjectionQuery(ServiceRequest arg0, java.lang.String arg1)` For internal use only - do not use this in your application.
`void`	`setEndpoint(java.lang.String endpoint)`

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

DGWSProxy

public DGWSProxy()

DGWSProxy

public DGWSProxy(java.lang.String endpoint)

Method Detail

getEndpoint

public java.lang.String getEndpoint()

setEndpoint

public void setEndpoint(java.lang.String endpoint)

getDGWS

public DGWS getDGWS()

closeStatefulQuery

public void closeStatefulQuery(ServiceRequest arg0)
                        throws java.rmi.RemoteException,
                               Exception

Description copied from interface: DGWS

Terminates the stateful query specified by the statefulQueryKey in the ServiceRequest object. When the query closes, the key is no longer valid to produce results so the key must be re-used to start a new query. For an overview, see "stateful searches" in the Discovery Gate Web Service Developer's Guide.

Specified by:: closeStatefulQuery in interface DGWS

Parameters:: arg0 - the service request
Throws:: java.rmi.RemoteException; Exception

convertStructureToMolfile

public java.lang.String[] convertStructureToMolfile(ServiceRequest arg0,
                                                    java.lang.String[] arg1)
                                             throws java.rmi.RemoteException

Description copied from interface: DGWS

Returns the array of molecules as an array of molfiles (or the array of reactions as an array of rxnfiles).

Supported molfile/rxnfile formats: SMILES and Chime string.
License access required: any valid license.

Specified by:: convertStructureToMolfile in interface DGWS

Parameters:: arg0 - the service request; arg1 - the array of structures to be converted
Returns:: the molfiles in the same order as the input structures
Throws:: java.rmi.RemoteException

findSourceMolecule

public ExistenceResult[] findSourceMolecule(ServiceRequest arg0,
                                            Datasource arg1,
                                            ExistenceRequest[] arg2)
                                     throws java.rmi.RemoteException,
                                            Exception

Description copied from interface: DGWS

Determines whether the molecules specified in the com.discoverygate.webservice.types.com.discoverygate.webservice.types.ExistenceRequest array exist in the source database.

Each request specifies both the structure and the user's own ID for the structure.
An com.discoverygate.webservice.types.com.discoverygate.webservice.types.ExistenceResult object
License access required: the target datasource.

Specified by:: findSourceMolecule in interface DGWS

Parameters:: arg0 - the service request; arg1 - a data source; arg2 - the molecules to search for
Returns:: an array of Molecules found and their IDs
Throws:: java.rmi.RemoteException; Exception

getCatalogsById

public CatalogResults getCatalogsById(ServiceRequest arg0,
                                      CatalogId[] arg1)
                               throws java.rmi.RemoteException,
                                      Exception

Description copied from interface: DGWS

Returns a CatalogsResults object (a list of Catalog objects) for a given list of Catalogs IDs.

The catalogs IDs can come from any of the procurement sources that the license-holder is entitled to.
The Catalog objects are of type Catalog, regardless of the source providing the object.
Each object can be inspected to discover the provider source.
License access required: ACD or SCD.

Specified by:: getCatalogsById in interface DGWS

Parameters:: arg0 - the service request; arg1 - the list of Catalog Id objects
Returns:: the CatalogResults object containing a list of Catalog objects
Throws:: java.rmi.RemoteException; Exception

getCatalogsByIdXML

public XMLResults getCatalogsByIdXML(ServiceRequest arg0,
                                     CatalogId[] arg1)
                              throws java.rmi.RemoteException,
                                     Exception

Description copied from interface: DGWS

Identical to the com.discoverygate.webservice.types.com.discoverygate.webservice.types.getCatalogsById method except that the results are returned in XML format.

Specified by:: getCatalogsByIdXML in interface DGWS

Parameters:: arg0 - the service request; arg1 - the list of Catalog ID objects
Returns:: an XML container for the CatalogResults object containing a list of Catalog objects
Throws:: java.rmi.RemoteException; Exception

getClassificationVocabulary

public ClassificationVocabulary getClassificationVocabulary(ServiceRequest arg0,
                                                            VocabularyVersion arg1)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Description copied from interface: DGWS

Returns the Classification vocabulary if the VocabularyVersion passed is not equal to the current server version.

The ClassificationVocabulary inherits VocabularyVersion. Therefore, the object can be serialized on the client-side to either return the latest version or to confirm that the holder already has the latest version.
sourceFilter of the ServiceRequest: supported.
License access required: Toxicity, CMC, or MDDR. The vocabulary contains items from Toxicity, Medicinal, and Drug databases depending on entitlement.

Specified by:: getClassificationVocabulary in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License; arg1 - the current version of the vocabulary held by caller
Returns:: the ClassificationVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary
Throws:: java.rmi.RemoteException; Exception

getClassificationVocabularyXML

public java.lang.String getClassificationVocabularyXML(ServiceRequest arg0,
                                                       VocabularyVersion arg1)
                                                throws java.rmi.RemoteException,
                                                       Exception

Description copied from interface: DGWS

Same as getClassificationVocabulary except that the vocabulary is returned as a string of XML.

Specified by:: getClassificationVocabularyXML in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License; arg1 - the current version of the vocabulary held by caller
Returns:: string of XML representing the ClassificationVocabulary object that contains either the vocabulary and related version id, or the current id and a null vocabulary
Throws:: java.rmi.RemoteException; Exception

getMoleculeSimilarity

public SimilarityResult[] getMoleculeSimilarity(ServiceRequest arg0,
                                                MoleculeId[] arg1,
                                                Structure arg2,
                                                SimilarityType arg3)
                                         throws java.rmi.RemoteException,
                                                Exception

Description copied from interface: DGWS

Returns the list of SimilarityResult (Molecule ID and similarity percentage) of the given IDs against the given structure, for the specified similarity type. The method can be used in conjuction with the results from a SIMILARITY-type structure search to find the similarity percentage of the hits returned.

Specified by:: getMoleculeSimilarity in interface DGWS

Parameters:: arg0 - the service request; arg1 - list of Molecule ID objects normally from the resultset of a previous search; arg2 - structure used in the comparison of the similarity search; arg3 - similarity type to use for the comparison
Returns:: list of Similairty results
Throws:: java.rmi.RemoteException; Exception

getMoleculeSourcesByMoleculeId

public MoleculeSourceResults getMoleculeSourcesByMoleculeId(ServiceRequest arg0,
                                                            Datasource arg1,
                                                            MoleculeId[] arg2)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Description copied from interface: DGWS

For a list of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeId's, determines which data sources contain the IDs. This method can be used for a fast lookup whether a given molecule or list of molecules exist in a given datasource.

Specified by:: getMoleculeSourcesByMoleculeId in interface DGWS

Parameters:: arg0 - the service request; arg1 - a data source to be searched. If set to null, all datasources of a given MoleculeId will be returned; arg2 - an array of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeId's
Returns:: a com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeSourceResults container with a list of com.discoverygate.webservice.types.com.discoverygate.webservice.types.MoleculeSource entities.
Throws:: java.rmi.RemoteException; Exception

getMoleculeSourcesByMoleculeIdXML

public XMLResults getMoleculeSourcesByMoleculeIdXML(ServiceRequest arg0,
                                                    Datasource arg1,
                                                    MoleculeId[] arg2)
                                             throws java.rmi.RemoteException,
                                                    Exception

Description copied from interface: DGWS

Identical to the com.discoverygate.webservice.types.com.discoverygate.webservice.types.getMoleculeSourcesByMoleculeId method except that the results returned are in XML format.

Specified by:: getMoleculeSourcesByMoleculeIdXML in interface DGWS

Parameters:: arg0 - the service request; arg1 - a data source to be searched. If set to null, all datasources of a given MoleculeId will be returned; arg2 - an array of MoleculeId's
Returns:: an XML results container with the MoleculeSourceResults
Throws:: java.rmi.RemoteException; Exception

getMoleculesByCatalogId

public MoleculeResults getMoleculesByCatalogId(ServiceRequest arg0,
                                               CatalogId arg1,
                                               BulkFineType arg2)
                                        throws java.rmi.RemoteException,
                                               Exception

Description copied from interface: DGWS

Returns the source molecules for a given CatalogId. The caller must specify whether the molecules returned should be available in BULK quantities, FINE quantities, or both BULK and FINE.

Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, and the ID_ONLY flag.
Licence access required: ACD or SCD.

Specified by:: getMoleculesByCatalogId in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License and retrieval flags.; arg1 - the catalog Id of the catalog to search; arg2 - the Bulk/Fine Flag used to filter the molecules from the catalog
Returns:: a molecule container
Throws:: java.rmi.RemoteException; Exception

getMoleculesByCatalogIdXML

public XMLResults getMoleculesByCatalogIdXML(ServiceRequest arg0,
                                             CatalogId arg1,
                                             BulkFineType arg2)
                                      throws java.rmi.RemoteException,
                                             Exception

Description copied from interface: DGWS

Same as getMoleculesByCatalogId except that the results are returned in XML format.

Specified by:: getMoleculesByCatalogIdXML in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License and retrieval flags.; arg1 - the catalog Id of the catalog to search; arg2 - the Bulk/Fine Flag used to filter the molecules from the catalog
Returns:: an XML results container
Throws:: java.rmi.RemoteException; Exception

getMoleculesByCatalogItem

public Molecule getMoleculesByCatalogItem(ServiceRequest arg0,
                                          CatalogItem[] arg1)
                                   throws java.rmi.RemoteException,
                                          Exception

Description copied from interface: DGWS

Returns a set of source molecules for the catalog items specified by the catalog numbers.

Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
Note: The source molecules automatically have the PROCUREMENT_PRICING flag specified. However, the sub-level data is already filtered to only show the product to which the catalog item is related.

Specified by:: getMoleculesByCatalogItem in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License; arg1 - the list of catalog items from the procurement database(s)
Returns:: a single molecule container that contains source molecules relating to the items requested
Throws:: java.rmi.RemoteException; Exception

getMoleculesByCatalogItemXML

public java.lang.String getMoleculesByCatalogItemXML(ServiceRequest arg0,
                                                     CatalogItem[] arg1)
                                              throws java.rmi.RemoteException,
                                                     Exception

Description copied from interface: DGWS

Same as getMoleculesByCatalogItem method except that the molecule container is returned as a string of XML.

Specified by:: getMoleculesByCatalogItemXML in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License; arg1 - the list of catalog items from the procurement database(s)
Returns:: a String of XML that contains source molecules relating to the items requested
Throws:: java.rmi.RemoteException; Exception

getMoleculesByCatalogNumbers

public MoleculeResults getMoleculesByCatalogNumbers(ServiceRequest arg0,
                                                    java.lang.String[] arg1)
                                             throws java.rmi.RemoteException,
                                                    Exception

Description copied from interface: DGWS

Returns the source molecules for a given CatalogIds.

Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, and the ID_ONLY flag.

Specified by:: getMoleculesByCatalogNumbers in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License and retrieval flags.; arg1 - the catalog Ids of the catalog to search
Returns:: a molecule container
Throws:: java.rmi.RemoteException; Exception

getMoleculesByCatalogNumbersXML

public XMLResults getMoleculesByCatalogNumbersXML(ServiceRequest arg0,
                                                  java.lang.String[] arg1)
                                           throws java.rmi.RemoteException,
                                                  Exception

Description copied from interface: DGWS

Same as getMoleculesByCatalogNumbers except that the results are returned in XML format.

Specified by:: getMoleculesByCatalogNumbersXML in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License and retrieval flags.; arg1 - the catalog Ids of the catalog to search
Returns:: an XML results container
Throws:: java.rmi.RemoteException; Exception

getMoleculesByClassification

public MoleculeResults getMoleculesByClassification(ServiceRequest arg0,
                                                    MoleculeSearch[] arg1,
                                                    java.lang.String arg2)
                                             throws java.rmi.RemoteException,
                                                    Exception

Description copied from interface: DGWS

Returns the molecules that are classified by the class-type passed and optionally conform to the structure search specified by the parameter aCriteria.

The aClass string passed must be one of those found in the classification vocabulary returned from getClassificationVocabulary (or getMoleculesByClassificationXML).
Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, ID_ONLY.
sourceFilter of the ServiceRequest: supported.
License access required: Toxicity, CMC or MDDR. Depending on your entitlements, the method will search Toxicity, Medicinal, and Drug-related information.

Specified by:: getMoleculesByClassification in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.; arg1 - the molecule search criteria by which to narrow the citations returned from the method. This argument can be null.; arg2 - the classification from the vocabulary on which to search, such as com.discoverygate.webservice.types.com.symyx.refdata.types.vocabulary.ClassificationVocabulary.
Returns:: the molecules that match the search criteria
Throws:: Exception; java.rmi.RemoteException

getMoleculesByClassificationXML

public XMLResults getMoleculesByClassificationXML(ServiceRequest arg0,
                                                  MoleculeSearch[] arg1,
                                                  java.lang.String arg2)
                                           throws java.rmi.RemoteException,
                                                  Exception

Description copied from interface: DGWS

Same as getMoleculesByClassification except that the results are returned in XML format.

Specified by:: getMoleculesByClassificationXML in interface DGWS

Parameters:: arg0 - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.; arg1 - the molecule search criteria by which to narrow the citations returned from the method; arg2 - the classification from the vocabulary on which to search
Returns:: the molecules that match the search criteria
Throws:: java.rmi.RemoteException; Exception

getMoleculesById

public MoleculeResults getMoleculesById(ServiceRequest arg0,
                                        MoleculeId[] arg1)
                                 throws java.rmi.RemoteException,
                                        Exception

Description copied from interface: DGWS

Returns an array of Molecule within a results container for the array of Molecule IDs.

The MoleculeId is a base class to many types of objects returned from the service. Therefore this method can consume the output from other methods without conversion.
The data retrieved from within the Molecule is controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags specified in the ServiceRequest object.
To control sub-level Reaction data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags.
Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags (and ReactionRetrievalFlags for sub-level Reaction data)
sourceFilter of the ServiceRequest: supported.

Specified by:: getMoleculesById in interface DGWS

Parameters:: arg0 - the service request; arg1 - the molecule IDs of the target molecules
Returns:: a results container with the Molecule hits
Throws:: java.rmi.RemoteException; Exception

getMoleculesByIdXML

public XMLResults getMoleculesByIdXML(ServiceRequest arg0,
                                      MoleculeId[] arg1)
                               throws java.rmi.RemoteException,
                                      Exception

Description copied from interface: DGWS

Identical to the com.discoverygate.webservice.types.getMoleculesById method except that the results returned are in XML format.

Specified by:: getMoleculesByIdXML in interface DGWS

Parameters:: arg0 - the service request; arg1 - the molecule IDs of the target molecules
Returns:: an XML results container with the Molecule hits
Throws:: java.rmi.RemoteException; Exception

getMoleculesByNames

public MoleculeResults getMoleculesByNames(ServiceRequest arg0,
                                           java.lang.String[] arg1)
                                    throws java.rmi.RemoteException,
                                           Exception

Description copied from interface: DGWS

Returns an array of

Molecule entities within a results container for the specified wildcard.
 The wildcard character '%' is used to specify multiple-character wildcards and the '_'
 for a single character wildcard.
 The name specified can be the chemical name, CAS number, NEMA key, or OHS name, and is case-insensitive
 To control the data retrieved from within the Molecule, specify com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags
 in the ServiceRequest object.
 To control sub-level Reaction data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags.
 
To control the number and offset of records retrieved, use the
 DataPage of the ServiceRequest object.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, ID_ONLY.
 sourceFilter of the ServiceRequest: supported.


Specified by:
getMoleculesByNames in interface DGWS


Parameters:
arg0 - the service request
arg1 - the search name with optional wildcard characters
Returns:
a results container with the Molecule hits
Throws:
java.rmi.RemoteException
Exception





getMoleculesByNamesXML
public XMLResults getMoleculesByNamesXML(ServiceRequest arg0,
                                         java.lang.String[] arg1)
                                  throws java.rmi.RemoteException,
                                         Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getMoleculesByName method except that the results returned are in XML format.


Specified by:
getMoleculesByNamesXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the search name with optional wildcard characters
Returns:
an XML results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getMoleculesByQuery
public MoleculeResults getMoleculesByQuery(ServiceRequest arg0,
                                           MoleculeSearch[] arg1,
                                           java.lang.String arg2)
                                    throws java.rmi.RemoteException,
                                           Exception

Description copied from interface: DGWS
For internal use only - do not use this in your application.


Specified by:
getMoleculesByQuery in interface DGWS



Throws:
java.rmi.RemoteException
Exception





getMoleculesByQueryXML
public XMLResults getMoleculesByQueryXML(ServiceRequest arg0,
                                         MoleculeSearch[] arg1,
                                         java.lang.String arg2)
                                  throws java.rmi.RemoteException,
                                         Exception

Description copied from interface: DGWS
For internal use only - do not use this in your application.


Specified by:
getMoleculesByQueryXML in interface DGWS



Throws:
java.rmi.RemoteException
Exception





getMoleculesBySourceId
public MoleculeResults getMoleculesBySourceId(ServiceRequest arg0,
                                              SourceId[] arg1)
                                       throws java.rmi.RemoteException,
                                              Exception

Description copied from interface: DGWS
Returns the top-level molecules that correspond to the list of SourceId objects.
 The IDs can be from any data source known to the service, including 3rd-party databases.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
 sourceFilter of the ServiceRequest: supported.
 


Specified by:
getMoleculesBySourceId in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, page parameters, and retrieval flags.
arg1 - the list of IDs for which the top-level molecules are to be retrieved
Returns:
a molecule results container
Throws:
java.rmi.RemoteException
Exception





getMoleculesBySourceIdMerged
public Molecule getMoleculesBySourceIdMerged(ServiceRequest arg0,
                                             SourceId[] arg1)
                                      throws java.rmi.RemoteException,
                                             Exception

Description copied from interface: DGWS
Returns an unpopulated Molecule container that contains source molecule objects, as well as their hierarchies
 fetched with the retrieval flags.
 Finds the source molecule information from the SourceId specified.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
 License access required: the specific datasource requested
 


Specified by:
getMoleculesBySourceIdMerged in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License and retrieval flags.
arg1 - the list of IDs for which to fetch the source molecules.
Returns:
a molecule container
Throws:
java.rmi.RemoteException
Exception





getMoleculesBySourceIdMergedXML
public java.lang.String getMoleculesBySourceIdMergedXML(ServiceRequest arg0,
                                                        SourceId[] arg1)
                                                 throws java.rmi.RemoteException,
                                                        Exception

Description copied from interface: DGWS
This method is the same as getMoleculeMergedBySourceId except that it returns the result as a single XML string.


Specified by:
getMoleculesBySourceIdMergedXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License and retrieval flags.
arg1 - the list of IDs for which to fetch the source molecules.
Returns:
a single XML string
Throws:
java.rmi.RemoteException
Exception
See Also:
getMoleculeMergedBySourceId





getMoleculesBySourceIdXML
public XMLResults getMoleculesBySourceIdXML(ServiceRequest arg0,
                                            SourceId[] arg1)
                                     throws java.rmi.RemoteException,
                                            Exception

Description copied from interface: DGWS
Same as getMoleculesBySourceId except that the results are returned in XML format.


Specified by:
getMoleculesBySourceIdXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, page parameters and retrieval flags.
arg1 - the list of IDs for which the top-level molecules are to be retrieved
Returns:
an XML results container
Throws:
java.rmi.RemoteException
Exception





getMoleculesByStructure
public MoleculeResults getMoleculesByStructure(ServiceRequest arg0,
                                               MoleculeSearch[] arg1)
                                        throws java.rmi.RemoteException,
                                               Exception

Description copied from interface: DGWS
Returns an array of Molecule within a results container that satisfy the query specified
 by a combination of the boolean structure searches within the aCriteria parameter.
 The data retrieved from within the Molecule is controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags
 specified in the ServiceRequest object.
 To control sub-level Reaction data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags.
 To control the number and offset of records retrieved, use the
 DataPage of the ServiceRequest object.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, ID_ONLY.
 sourceFilter of the ServiceRequest: supported.
 License access required: at least one Reaction datasource.


Specified by:
getMoleculesByStructure in interface DGWS


Parameters:
arg0 - the service request
arg1 - the structure search combination
Returns:
a results container with the Molecule hits
Throws:
java.rmi.RemoteException
Exception





getMoleculesByStructureXML
public XMLResults getMoleculesByStructureXML(ServiceRequest arg0,
                                             MoleculeSearch[] arg1)
                                      throws java.rmi.RemoteException,
                                             Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getMoleculesByStructure except that the results returned are in XML format.


Specified by:
getMoleculesByStructureXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the structure search combination
Returns:
an XML results container with the Molecule hits in XML format
Throws:
java.rmi.RemoteException
Exception





getMoleculesFilterInfoById
public AvailabilityFilterResults getMoleculesFilterInfoById(ServiceRequest arg0,
                                                            MoleculeId[] arg1)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Description copied from interface: DGWS
Returns an array of AvailabilityFilter within a results container for the given array of Molecule IDs


Specified by:
getMoleculesFilterInfoById in interface DGWS


Parameters:
arg0 - the service request
arg1 - the molecule IDs
Returns:
a results container
Throws:
java.rmi.RemoteException
Exception





getMoleculesFilterInfoByIdXML
public XMLResults getMoleculesFilterInfoByIdXML(ServiceRequest arg0,
                                                MoleculeId[] arg1)
                                         throws java.rmi.RemoteException,
                                                Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getMoleculesFilterInfoById method except
 that the results returned are in XML format.

 Returns an array of AvailabilityFilter within a results container for the given array of Molecule IDs


Specified by:
getMoleculesFilterInfoByIdXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the molecule IDs
Returns:
an XML results container with the AvailabilityFilterResults
Throws:
java.rmi.RemoteException
Exception





getPatentsByTitle
public PatentResults getPatentsByTitle(ServiceRequest arg0,
                                       java.lang.String arg1)
                                throws java.rmi.RemoteException,
                                       Exception

Description copied from interface: DGWS
Returns the Patent entities (DGWS classes) that match the search criteria passed in the aTextQuery  parameter.
 The search criteria must be in the form of an Oracle text query and therefore can contain single words, groups of words (found as a group),
 or boolean logic such as "ligand and inhibitor", which would search titles that contain both 'ligand' and 'inhibitor' in any order.
 Flag support: Molecule Retrieval Flags that are drug-related.
 License access required: MDDR.
 


Specified by:
getPatentsByTitle in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags required
arg1 - search criteria in the form of an Oracle text query
Returns:
the reactions that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getPatentsByTitleXML
public XMLResults getPatentsByTitleXML(ServiceRequest arg0,
                                       java.lang.String arg1)
                                throws java.rmi.RemoteException,
                                       Exception

Description copied from interface: DGWS
The same as getPatentsByTitle except that the response is returned in XML form.


Specified by:
getPatentsByTitleXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required
arg1 - search criteria in the form of an Oracle text query
Returns:
the reactions that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getProcurementVocabulary
public ProcurementVocabularies getProcurementVocabulary(ServiceRequest arg0,
                                                        VocabularyVersion arg1)
                                                 throws java.rmi.RemoteException,
                                                        ServiceFault

Description copied from interface: DGWS
Returns the ProcurementVocabularies object if the VocabularyVersion passed is not equal to the current server version.
 The ProcurementVocabularies object inherits VocabularyVersion. Therefore, the object can be serialized on the client-side to
 either return the latest version or to confirm that the holder already has the latest version.
 The vocabulary contains a ProcurementVocabulary object for each procurement database the caller has access to.
 sourceFilter of the ServiceRequest: supported.
 License access required: ACD and/or SCD.
 


Specified by:
getProcurementVocabulary in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the current version of the vocabulary held by caller
Returns:
the ProcurementVocabularies object that either contains the vocabularies and related version id, or the current id and a null vocabulary list
Throws:
java.rmi.RemoteException
Exception
ServiceFault





getProcurementVocabularyXML
public java.lang.String getProcurementVocabularyXML(ServiceRequest arg0,
                                                    VocabularyVersion arg1)
                                             throws java.rmi.RemoteException,
                                                    Exception

Description copied from interface: DGWS
Same as getProcurementVocabulary except that the vocabulary is returned as a string of XML.


Specified by:
getProcurementVocabularyXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the current version of the vocabulary held by caller
Returns:
a string of XML that represents the ProcurementVocabulary object that contains either the vocabulary  and related version id, or the current id and a null vocabulary
Throws:
java.rmi.RemoteException
Exception





getProductsByMoleculeAndSuppliers
public ProductResults getProductsByMoleculeAndSuppliers(ServiceRequest arg0,
                                                        SourceId[] arg1,
                                                        SupplierId[] arg2)
                                                 throws java.rmi.RemoteException,
                                                        Exception

Description copied from interface: DGWS
Returns an array of Product within a results container for the given array of Molecule IDs
 and Supplier IDs.
 The MoleculeId is a base class to many types of objects returned from the service.
 Therefore this method can consume the output from other methods without conversion.
 The data retrieved is NOT controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags. Therefore all
 Packages and Catalogs for each Product hit by the search are returned.
 The DataPage of the ServiceRequest object is ignored and all Products
 that match the criteria are returned.
 License access required: ACD or SCD
 


Specified by:
getProductsByMoleculeAndSuppliers in interface DGWS


Parameters:
arg0 - the service request
arg1 - the molecule IDs of the target molecules
arg2 - the supplier IDs of the target Companies
Returns:
a results container with the Product hits
Throws:
java.rmi.RemoteException
Exception





getProductsByMoleculeAndSuppliersXML
public XMLResults getProductsByMoleculeAndSuppliersXML(ServiceRequest arg0,
                                                       SourceId[] arg1,
                                                       SupplierId[] arg2)
                                                throws java.rmi.RemoteException,
                                                       Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getProductsByMoleculeandSuppliers method except
 that the results returned are in XML format.


Specified by:
getProductsByMoleculeAndSuppliersXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the molecule IDs of the target molecules
arg2 - the supplier IDs of the target Companies
Returns:
an XML results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionCitations
public RxnCitationResults getReactionCitations(ServiceRequest arg0,
                                               CitationCriteria arg1)
                                        throws java.rmi.RemoteException,
                                               Exception

Description copied from interface: DGWS
Returns the Reaction citation entities (DGWS classes) that conform to the citation criteria passed to the method.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags, and therefore the caller is able to create a hierarchy from the results with citations on top.
 sourceFilter of the ServiceRequest: supported.
 License access required: any reaction database.
 


Specified by:
getReactionCitations in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required
arg1 - the criteria on which to narrow the citations returned from the method
Returns:
the Citations that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getReactionCitationsXML
public XMLResults getReactionCitationsXML(ServiceRequest arg0,
                                          CitationCriteria arg1)
                                   throws java.rmi.RemoteException,
                                          Exception

Description copied from interface: DGWS
Same as getReactionCitations except that the result are returned in XML format


Specified by:
getReactionCitationsXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required
arg1 - the criteria by which to narrow the citations returned from the method
Returns:
the Citations that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getReactionClassification
public Classification[] getReactionClassification(ServiceRequest arg0,
                                                  Structure[] arg1)
                                           throws java.rmi.RemoteException,
                                                  Exception

Description copied from interface: DGWS
Returns an object containing the Broad, Medium and Narrow InfoChem class-codes
 for each rxnfile given in the array.
 The Structure is a base class to many types of objects returned from the service.
 Therefore this method can consume the output from other methods without conversion.
 License access required: at least one Reaction datasource.


Specified by:
getReactionClassification in interface DGWS


Parameters:
arg0 - the service request
arg1 - an array of RxnFile reaction structures
Returns:
an object containing class-codes
Throws:
java.rmi.RemoteException
Exception





getReactionVocabulary
public ReactionVocabulary getReactionVocabulary(ServiceRequest arg0,
                                                VocabularyVersion arg1)
                                         throws java.rmi.RemoteException,
                                                Exception

Description copied from interface: DGWS
Returns the Reaction vocabulary if the VocabularyVersion passed is not equal to the current server version.
 The ReactionVocabulary inherits VocabularyVersion.
 Therefore, the object can be serialzied on the client-side to
 return the latest version or confirm that the holder already has the latest version.
 The vocabulary contains items only from those reaction databases the caller has access to.
 sourceFilter of the ServiceRequest: supported.
 License access required: any reaction database.
 


Specified by:
getReactionVocabulary in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the current version of the vocabulary held by caller
Returns:
the ReactionVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary
Throws:
java.rmi.RemoteException
Exception





getReactionVocabularyXML
public java.lang.String getReactionVocabularyXML(ServiceRequest arg0,
                                                 VocabularyVersion arg1)
                                          throws java.rmi.RemoteException,
                                                 Exception

Description copied from interface: DGWS
Same as getReactionVocabulary except that the vocabulary is returned as a string of XML.


Specified by:
getReactionVocabularyXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the current version of the vocabulary held by caller
Returns:
a string of XML that represents the ReactionVocabulary object that either contains the
 vocabulary and related version id, or the current id and a null vocabulary
Throws:
java.rmi.RemoteException
Exception





getReactionsById
public ReactionResults getReactionsById(ServiceRequest arg0,
                                        ReactionId[] arg1)
                                 throws java.rmi.RemoteException,
                                        Exception

Description copied from interface: DGWS
Returns an array of Reaction within a results container for the array of Reaction IDs.
 The ReactionId is a base class to many types of objects returned from the service.
 Therefore this method can consume the output from other methods without conversion.
 To control the data retrieved from within the Reaction, specify com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags
 in the ServiceRequest object.
 To control sub-level Molecule data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags
 Flag support: ReactionRetrievalFlags (and MoleculeRetrievalFlags for sub-level Molecule data)
 sourceFilter of the ServiceRequest: supported.
 License access required: at least one Reaction datasource.


Specified by:
getReactionsById in interface DGWS


Parameters:
arg0 - the service request
arg1 - the reaction IDs of the target reactions
Returns:
a results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionsByIdXML
public XMLResults getReactionsByIdXML(ServiceRequest arg0,
                                      ReactionId[] arg1)
                               throws java.rmi.RemoteException,
                                      Exception

Description copied from interface: DGWS
Identical to the getReactionsById method except that the results returned are in XML format.


Specified by:
getReactionsByIdXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the reaction IDs of the target reactions
Returns:
an XML results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionsByProduct
public ReactionResults getReactionsByProduct(ServiceRequest arg0,
                                             MoleculeSearch[] arg1,
                                             RxnProductCriteria arg2)
                                      throws java.rmi.RemoteException,
                                             Exception

Description copied from interface: DGWS
Gets the reactions where at least one of the products conforms to the search created from the MoleculeSearch[] passed to the method.
 The reactions returned can be further filtered on the product yield by passing a RxnProductCriteria object.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags, ID_ONLY flag.
 sourceFilter of the ServiceRequest: supported.
 License access required: any reaction database.
 


Specified by:
getReactionsByProduct in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required
arg1 - the array of MoleculeSearch objects that describes how to search the products (optional)
arg2 - the criteria for which to narrow the candidate products. This parameter can be null.
Returns:
the reactions that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getReactionsByProductXML
public XMLResults getReactionsByProductXML(ServiceRequest arg0,
                                           MoleculeSearch[] arg1,
                                           RxnProductCriteria arg2)
                                    throws java.rmi.RemoteException,
                                           Exception

Description copied from interface: DGWS
The same as getReactionsByProduct except that the response is returned in XML form.


Specified by:
getReactionsByProductXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags required
arg1 - the array of MoleculeSearch objects that describes how to search the products (optional)
arg2 - the criteria by which to narrow the candidate products. This parameter can be null.
Returns:
the reactions that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getReactionsByQuery
public ReactionResults getReactionsByQuery(ServiceRequest arg0,
                                           ReactionSearch[] arg1,
                                           java.lang.String arg2)
                                    throws java.rmi.RemoteException,
                                           Exception

Description copied from interface: DGWS
For internal use only - do not use this in your application.


Specified by:
getReactionsByQuery in interface DGWS



Throws:
java.rmi.RemoteException
Exception





getReactionsByQueryXML
public XMLResults getReactionsByQueryXML(ServiceRequest arg0,
                                         ReactionSearch[] arg1,
                                         java.lang.String arg2)
                                  throws java.rmi.RemoteException,
                                         Exception

Description copied from interface: DGWS
For internal use only - do not use this in your application.


Specified by:
getReactionsByQueryXML in interface DGWS



Throws:
java.rmi.RemoteException
Exception





getReactionsByStructure
public ReactionResults getReactionsByStructure(ServiceRequest arg0,
                                               ReactionSearch[] arg1)
                                        throws java.rmi.RemoteException,
                                               Exception

Description copied from interface: DGWS
Returns an array of Reaction within a results container that satisfy the query specified.
 The data retrieved from within the Reaction is controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags
 specified in the ServiceRequest object.
 To control sub-level Molecule data returned, specify the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags
 To control the number and offset of records retrieved, use the
 DataPage of the ServiceRequest object
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags, ID_ONLY.
 sourceFilter of the ServiceRequest: supported.
 License access required: at least one Reaction datasource.


Specified by:
getReactionsByStructure in interface DGWS


Parameters:
arg0 - the service request
arg1 - the structure search combination
Returns:
a results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionsByStructureXML
public XMLResults getReactionsByStructureXML(ServiceRequest arg0,
                                             ReactionSearch[] arg1)
                                      throws java.rmi.RemoteException,
                                             Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getReactionsByStructure except that the results returned are in XML format.


Specified by:
getReactionsByStructureXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the structure search combination
Returns:
an XML results container with the Reaction hits in XML format
Throws:
java.rmi.RemoteException
Exception





getReactionsByVariation
public ReactionResults getReactionsByVariation(ServiceRequest arg0,
                                               RxnVariationId[] arg1)
                                        throws java.rmi.RemoteException,
                                               Exception

Description copied from interface: DGWS
Identical to the getReactionsById method except that the VariationId is specified.


Specified by:
getReactionsByVariation in interface DGWS


Parameters:
arg0 - the service request
arg1 - the reaction validation IDs of the target reactions
Returns:
a results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionsByVariationXML
public XMLResults getReactionsByVariationXML(ServiceRequest arg0,
                                             RxnVariationId[] arg1)
                                      throws java.rmi.RemoteException,
                                             Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getReactionsByVariation method except that the results returned are in XML format.


Specified by:
getReactionsByVariationXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the reaction variation IDs of the target reactions
Returns:
an XML results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionsFilterInfoById
public ReactionFilterResults getReactionsFilterInfoById(ServiceRequest arg0,
                                                        ReactionId[] arg1)
                                                 throws java.rmi.RemoteException,
                                                        Exception

Description copied from interface: DGWS
Returns an array of RxnFilterVariation within a results container for the array of Reaction IDs.
 The ReactionId is a base class to many types of objects returned from the service.
 Therefore this method can consume the output from other methods without conversion.
 To control the data retrieved from within the RxnFilterVariation, specify com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags
 in the ServiceRequest object.
 Flag support: ReactionRetrievalFlags
 License access required: at least one Reaction datasource.


Specified by:
getReactionsFilterInfoById in interface DGWS


Parameters:
arg0 - the service request
arg1 - the reaction IDs of the target reactions
Returns:
a results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getReactionsFilterInfoByIdXML
public XMLResults getReactionsFilterInfoByIdXML(ServiceRequest arg0,
                                                ReactionId[] arg1)
                                         throws java.rmi.RemoteException,
                                                Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getReactionsFilterInfoById method except
 that the results returned are in XML format.
 Returns an array of RxnFilterVariation within a results container for the given array of Reaction IDs


Specified by:
getReactionsFilterInfoByIdXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the Reaction IDs
Returns:
an XML results container with the ReactionFilterResults
Throws:
java.rmi.RemoteException
Exception





getSchema
public java.lang.String getSchema(ServiceRequest arg0,
                                  SchemaType arg1)
                           throws java.rmi.RemoteException,
                                  Exception

Description copied from interface: DGWS
Returns the Schema (XSD format) of the root-level object specified in the SchemaType.
 Note: If the Type chosen is the complete object, the parameters of the ServiceRequest are ignored and the entire schema is retrieved.
 Otherwise the schema returned supports the flags and the sourceFilter specified in the ServiceRequest object.


Specified by:
getSchema in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the type of schema to be returned
Returns:
the Schema XML in XSD format
Throws:
java.rmi.RemoteException
Exception





getServiceInformation
public ServiceInformation getServiceInformation(ServiceRequest arg0)
                                         throws java.rmi.RemoteException

Description copied from interface: DGWS
Returns information associated with the license, such as the version string of the service,
 a list of retrieval flags, a list of sources and their copyright strings.
 See ServiceInformation.
 This method is typically the first method called against the service.


Specified by:
getServiceInformation in interface DGWS


Parameters:
arg0 - the service request
Returns:
the ServiceInformation object
Throws:
java.rmi.RemoteException





getSourceMoleculeSimilarity
public SimilaritySourceResult[] getSourceMoleculeSimilarity(ServiceRequest arg0,
                                                            SourceId[] arg1,
                                                            Structure arg2,
                                                            SimilarityType arg3)
                                                     throws java.rmi.RemoteException,
                                                            Exception

Description copied from interface: DGWS
Operates in the same way as getMoleculeSimilarity
 except that the inputs and outputs are related to source molecule IDs.
 License access required: the specific datasource requested.
 


Specified by:
getSourceMoleculeSimilarity in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the list of source Id objects by which to compare for percentage similarity
arg2 - the structure used for comparison
arg3 - the type of simiarity to use for comparison
Returns:
a result container
Throws:
java.rmi.RemoteException
Exception
See Also:
getMoleculeSimilarity





getSourceMoleculesByStructure
public MoleculeResults getSourceMoleculesByStructure(ServiceRequest arg0,
                                                     MoleculeSearch[] arg1,
                                                     Datasource arg2)
                                              throws java.rmi.RemoteException,
                                                     Exception

Description copied from interface: DGWS
Searches the source database specified by the Datasource parameter for the MoleculeSearch criteria.
 The results are added into the Molecule object at the source molecule level.
 The top-level data is not retrieved.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags that relate to the source being searched, and the ID_ONLY flag.
 A licence with access to the specific datasource requested is required by this method.
 


Specified by:
getSourceMoleculesByStructure in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page, Molecule, and com.discoverygate.webservice.types.com.symyx.refdata.types.ReactionRetrievalFlags
arg1 - the molecule search criteria by which to narrow the citations returned from the method
arg2 - the source database on which to search
Returns:
a molecule container
Throws:
java.rmi.RemoteException
Exception





getSourceMoleculesByStructureXML
public XMLResults getSourceMoleculesByStructureXML(ServiceRequest arg0,
                                                   MoleculeSearch[] arg1,
                                                   Datasource arg2)
                                            throws java.rmi.RemoteException,
                                                   Exception

Description copied from interface: DGWS
Same as getSourceMoleculesByStructure except that the results are returned in XML format.


Specified by:
getSourceMoleculesByStructureXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the molecule search criteria by which to narrow the citations returned from the method
arg2 - the source database on which to search
Throws:
java.rmi.RemoteException
Exception





getSourceSummaryByMoleculeId
public MoleculeSourceResults getSourceSummaryByMoleculeId(ServiceRequest arg0,
                                                          Datasource[] arg1,
                                                          MoleculeId[] arg2)
                                                   throws java.rmi.RemoteException,
                                                          Exception

Description copied from interface: DGWS
Determines the for a list of MoleculeId's in which data sources they exist.
 This method can be used for a fast lookup whether a given molecule or list of molecules
 exist in a given datasource.
 This method is provides the exact same result as com.discoverygate.webservice.types.getMoleculeSourcesByMoleculeId, except that it accepts an array
 of datasources instead of just a single datasource.


Specified by:
getSourceSummaryByMoleculeId in interface DGWS


Parameters:
arg0 - the service request
arg1 - an array Datasource to be searched. If set to null, all datasources of a given MoleculeId will be returned
arg2 - an array of MoleculeId's
Returns:
a MoleculeSourceResults container with a list of MoleculeSource entities.
Throws:
java.rmi.RemoteException
Exception





getSourceSummaryByMoleculeIdXML
public XMLResults getSourceSummaryByMoleculeIdXML(ServiceRequest arg0,
                                                  Datasource[] arg1,
                                                  MoleculeId[] arg2)
                                           throws java.rmi.RemoteException,
                                                  Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getSourceSummaryByMoleculeId method except
 that the results returned are in XML format.


Specified by:
getSourceSummaryByMoleculeIdXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - an array Datasource to be searched. If set to null, all datasources of a given MoleculeId will be returned
arg2 - an array of MoleculeId's
Returns:
an XML results container with the MoleculeSourceResults
Throws:
java.rmi.RemoteException
Exception





getSuppliers
public SupplierResults[] getSuppliers(ServiceRequest arg0,
                                      java.lang.String arg1)
                               throws java.rmi.RemoteException,
                                      Exception

Description copied from interface: DGWS
Returns an array of com.discoverygate.webservice.types.Supplier within a results container for the specified wildcard and procurement datasource.
 Depending on the licensee's entitlement, this method can return more than one results container, one for each procurement source.
 Each results container specifies the datasource of the results contained within it.
 The wildcard character '%' is used to specify multiple-character wildcards and the '_'
 for a single character wildcard.
 The name specified is that of the full company name and is case-insensitive.
 The data retrieved is NOT controlled by the com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags, and therefore the data returned
 differs from the Supplier retrieval flag in that the associated Distributor information is associated
 with each Supplier.
 To control the number and offset of records retrieved, use the
 DataPage of the ServiceRequest object.
sourceFilter of the ServiceRequest: supported.
 License access required: the procurement datasource presented.
 


Specified by:
getSuppliers in interface DGWS


Parameters:
arg0 - the service request
arg1 - the search name, with optional wildcard characters, which can be null
Returns:
a results container with the Molecule hits
Throws:
java.rmi.RemoteException
Exception





getSuppliersById
public SupplierResults getSuppliersById(ServiceRequest arg0,
                                        SupplierId[] arg1)
                                 throws java.rmi.RemoteException,
                                        Exception

Description copied from interface: DGWS
Returns a SupplierResults object (a list of Supplier objects) for a given list of Supplier IDs.
 The supplier IDs can come from any of the procurement sources that the license-holder is entitled to.
 The Supplier objects are of type Supplier regardless of the source providing the object.
 Each object can be inspected to discover the provider source.
 Note: The method serializes all of the Company entity (DGWS class), and therefore both the Catalog and Distributors are included in the Company data.
 License access required: ACD or SCD.
 


Specified by:
getSuppliersById in interface DGWS


Parameters:
arg0 - the service request
arg1 - the list of Supplier ID objects
Returns:
the SupplierResults object containing a list of Supplier objects
Throws:
java.rmi.RemoteException
Exception





getSuppliersByIdXML
public XMLResults getSuppliersByIdXML(ServiceRequest arg0,
                                      SupplierId[] arg1)
                               throws java.rmi.RemoteException,
                                      Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getSuppliersById method except that the results are returned in XML format.


Specified by:
getSuppliersByIdXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the list of Supplier ID objects
Returns:
the SupplierResults object containing a list of Supplier objects
Throws:
java.rmi.RemoteException
Exception





getSuppliersXML
public XMLResults[] getSuppliersXML(ServiceRequest arg0,
                                    java.lang.String arg1)
                             throws java.rmi.RemoteException,
                                    Exception

Description copied from interface: DGWS
Identical to the com.discoverygate.webservice.types.getSuppliers method except that the results returned are in XML format.


Specified by:
getSuppliersXML in interface DGWS


Parameters:
arg0 - the service request
arg1 - the search name with optional wildcard characters
Returns:
an XML results container with the Reaction hits
Throws:
java.rmi.RemoteException
Exception





getToxicityExperiments
public ExperimentResults getToxicityExperiments(ServiceRequest arg0,
                                                MoleculeSearch[] arg1,
                                                ExperimentCriteria arg2)
                                         throws java.rmi.RemoteException,
                                                Exception

Description copied from interface: DGWS
Returns the toxicity experiments that conform to the experiment criteria passed, and optionally conform to the structure search specified by the parameter aSearch.
 Flag support: com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags related to Toxicity data.
 License access required: Toxicity.
 


Specified by:
getToxicityExperiments in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
arg1 - the molecule search criteria by which to narrow the citations returned from the method. This argument can be null.
arg2 - the classification from the vocabulary on which to search
Returns:
the molecules that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getToxicityExperimentsXML
public XMLResults getToxicityExperimentsXML(ServiceRequest arg0,
                                            MoleculeSearch[] arg1,
                                            ExperimentCriteria arg2)
                                     throws java.rmi.RemoteException,
                                            Exception

Description copied from interface: DGWS
Same as getToxicityExperiments except that the results are returned in XML format


Specified by:
getToxicityExperimentsXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License, Page information, and com.discoverygate.webservice.types.com.symyx.refdata.types.MoleculeRetrievalFlags.
arg1 - the molecule search criteria by which to narrow the citations returned from the method
arg2 - the classification from the vocabulary on which to search
Returns:
the molecules that match the search criteria
Throws:
java.rmi.RemoteException
Exception





getToxicityPublications
public ToxPublication[] getToxicityPublications(ServiceRequest arg0,
                                                ToxCoden[] arg1)
                                         throws java.rmi.RemoteException

Description copied from interface: DGWS
Returns a list of Toxicology publication objects for the Codens passed to the method.
 
 These codens normally originate from the toxiciology information returned when using the
 MoleculeRetrievalFlags.LITERATURE flag.
 License access required: Toxicity.
 


Specified by:
getToxicityPublications in interface DGWS


Parameters:
arg0 - the service request
arg1 - the codens
Returns:
a list of Publication objects from the Toxicology source database
Throws:
java.rmi.RemoteException





getToxicityVocabulary
public ToxicityVocabulary getToxicityVocabulary(ServiceRequest arg0,
                                                VocabularyVersion arg1)
                                         throws java.rmi.RemoteException

Description copied from interface: DGWS
Returns the Toxicity vocabulary if the VocabularyVersion passed is not equal to the current server version.
 The ToxicityVocabulary inherits VocabularyVersion.
 Therefore, the object can be serialized on the client-side to
 either return the latest version or to confirm that the holder already has the latest version.
 License access required: Toxicity.
 


Specified by:
getToxicityVocabulary in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the current version of the vocabulary held by caller
Returns:
the ToxicityVocabulary object that either contains the vocabulary and related version id, or the current id and a null vocabulary
Throws:
java.rmi.RemoteException





getToxicityVocabularyXML
public java.lang.String getToxicityVocabularyXML(ServiceRequest arg0,
                                                 VocabularyVersion arg1)
                                          throws java.rmi.RemoteException

Description copied from interface: DGWS
Same as getToxicityVocabulary except that the vocabulary is returned as a string of XML.


Specified by:
getToxicityVocabularyXML in interface DGWS


Parameters:
arg0 - the ServiceRequest describing at least the License
arg1 - the current version of the vocabulary held by caller
Returns:
a string of XML that represents the ToxicityVocabulary object that contains the vocabulary and related version id, or the current id and a null vocabulary
Throws:
java.rmi.RemoteException





runProjectionQuery
public XMLResults runProjectionQuery(ServiceRequest arg0,
                                     java.lang.String arg1)
                              throws java.rmi.RemoteException,
                                     Exception

Description copied from interface: DGWS
For internal use only - do not use this in your application.


Specified by:
runProjectionQuery in interface DGWS



Throws:
java.rmi.RemoteException
Exception














  
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com.discoverygate.webservice Class DGWSProxy

DGWSProxy

DGWSProxy

getEndpoint

setEndpoint

getDGWS

closeStatefulQuery

convertStructureToMolfile

findSourceMolecule

getCatalogsById

getCatalogsByIdXML

getClassificationVocabulary

getClassificationVocabularyXML

getMoleculeSimilarity

getMoleculeSourcesByMoleculeId

getMoleculeSourcesByMoleculeIdXML

getMoleculesByCatalogId

getMoleculesByCatalogIdXML

getMoleculesByCatalogItem

getMoleculesByCatalogItemXML

getMoleculesByCatalogNumbers

getMoleculesByCatalogNumbersXML

getMoleculesByClassification

getMoleculesByClassificationXML

getMoleculesById

getMoleculesByIdXML

getMoleculesByNames

getMoleculesByNamesXML

getMoleculesByQuery

getMoleculesByQueryXML

getMoleculesBySourceId

getMoleculesBySourceIdMerged

getMoleculesBySourceIdMergedXML

getMoleculesBySourceIdXML

getMoleculesByStructure

getMoleculesByStructureXML

getMoleculesFilterInfoById

getMoleculesFilterInfoByIdXML

getPatentsByTitle

getPatentsByTitleXML

getProcurementVocabulary

getProcurementVocabularyXML

getProductsByMoleculeAndSuppliers

getProductsByMoleculeAndSuppliersXML

getReactionCitations

getReactionCitationsXML

getReactionClassification

getReactionVocabulary

getReactionVocabularyXML

getReactionsById

getReactionsByIdXML

getReactionsByProduct

getReactionsByProductXML

getReactionsByQuery

getReactionsByQueryXML

getReactionsByStructure

getReactionsByStructureXML

getReactionsByVariation

getReactionsByVariationXML

getReactionsFilterInfoById

getReactionsFilterInfoByIdXML

getSchema

getServiceInformation

getSourceMoleculeSimilarity

getSourceMoleculesByStructure

getSourceMoleculesByStructureXML

getSourceSummaryByMoleculeId

getSourceSummaryByMoleculeIdXML

getSuppliers

getSuppliersById

getSuppliersByIdXML

getSuppliersXML

getToxicityExperiments

getToxicityExperimentsXML

getToxicityPublications

getToxicityVocabulary

getToxicityVocabularyXML

runProjectionQuery

com.discoverygate.webservice
Class DGWSProxy