Uses of Class
ambit2.db.search.AbstractQuery

Packages that use AbstractQuery

Package	Description
ambit2.db.cache
ambit2.db.chemrelation
ambit2.db.readers
ambit2.db.search
ambit2.db.search.property
ambit2.db.search.qlabel
ambit2.db.search.structure
ambit2.db.search.structure.byproperty
ambit2.db.search.structure.pairwise
ambit2.db.simiparity.space
ambit2.db.substance
ambit2.db.substance.ids
ambit2.db.substance.relation
ambit2.db.substance.study
ambit2.db.update.bookmark
ambit2.db.update.bundle
ambit2.db.update.bundle.chemicals
ambit2.db.update.bundle.effects
ambit2.db.update.bundle.endpoints
ambit2.db.update.bundle.matrix
ambit2.db.update.bundle.substance
ambit2.db.update.dataset
ambit2.db.update.fp
ambit2.db.update.model
ambit2.db.update.property
ambit2.db.update.propertyannotations
ambit2.db.update.queryfolder
ambit2.db.update.reference
ambit2.db.update.storedquery
ambit2.db.update.structure
ambit2.db.version
ambit2.dbui

Uses of AbstractQuery in ambit2.db.cache

Subclasses of AbstractQuery in ambit2.db.cache

Modifier and Type	Class and Description
class	QueryCachedResults<T>
class	QueryCachedResultsBoolean Returns results of a previously executed query (e.g.
class	RetrieveStructureImagePath Cached images

Uses of AbstractQuery in ambit2.db.chemrelation

Subclasses of AbstractQuery in ambit2.db.chemrelation

Modifier and Type	Class and Description
class	ReadDatasetRelation Similar to ReadStructureRelation , but retrieves the related compounds for the entire dataset
class	ReadStructureRelation

Uses of AbstractQuery in ambit2.db.readers

Subclasses of AbstractQuery in ambit2.db.readers

Modifier and Type	Class and Description
class	AbstractStructureRetrieval<R> Retrieve structures, given a chemical or structure ID.
class	ReadChemicalIds
class	RetrieveAtomContainer
class	RetrieveDatasets
class	RetrieveDescriptor
class	RetrieveField<ResultType>
class	RetrieveFieldPropertyValue Retrive property-value pairs
class	RetrieveFieldStructure Retrieve property value pairs and assign to a structure record
class	RetrieveGroupedValuesByAlias
class	RetrieveModelTemplates<ResultType> Retrieves property values given a model
class	RetrieveModelTemplatesPropertyValue Retrieves property values given a model
class	RetrieveProfileValues
class	RetrieveProfileValuesAsRow
class	RetrieveStructure
class	RetrieveTemplate<ResultType>
class	RetrieveTemplatePropertyValue Retrieves properties by given template
class	RetrieveTemplateStructure

Uses of AbstractQuery in ambit2.db.search

Subclasses of AbstractQuery in ambit2.db.search

Modifier and Type	Class and Description
class	DictionaryObjectQuery
class	DictionaryQuery<T extends Dictionary>
class	DictionarySubjectQuery
class	QueryExperiment<T,C extends net.idea.modbcum.i.IQueryCondition,ResultType>
class	QuerySmilesByID
class	QueryUser Searches in users table

Uses of AbstractQuery in ambit2.db.search.property

Subclasses of AbstractQuery in ambit2.db.search.property

Modifier and Type	Class and Description
class	AbstractPropertyRetrieval<F,T,C extends net.idea.modbcum.i.IQueryCondition>
class	FreeTextPropertyQuery Same as FreeTextQuery , but retrieves properties
class	ModelTemplates
class	PropertiesByDataset Retrieves Property-es used by particular dataset
class	PropertiesByQuery
class	PropertyCount
class	PropertyRange Returns binned range of property (defined by Fieldname), number of bins is given by setValue()
class	PropertyStatsNumeric
class	PropertyStatsString
class	QueryMetricRange
class	QueryOntology
class	QueryPairwiseTanimoto Generatise pairwise similarities between structures in given datasets
class	QueryPairwiseTanimotoAndProperty Similar to QueryPairwiseTanimoto , but returns also property values
class	RetieveFeatures Given IStructureRecord , find if its properties are already in the properties table.
class	RetrieveFieldNames
class	RetrieveFieldNamesByAlias Finds properties by alias
class	RetrieveFieldNamesByType Retrieve names of string properties if setValue(0) ; real valued properties if setValue(1) int properties if setValue(2)
class	RetrieveProfile
class	TemplateQuery

Uses of AbstractQuery in ambit2.db.search.qlabel

Subclasses of AbstractQuery in ambit2.db.search.qlabel

Modifier and Type	Class and Description
class	QueryConsensus
class	QueryQLabel

Uses of AbstractQuery in ambit2.db.search.structure

Subclasses of AbstractQuery in ambit2.db.search.structure

Modifier and Type	Class and Description
class	AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition>
class	ChemicalByQueryFolder Retrieves chemicals from set of datasets, defined in the query table restricted by sessions.title
class	FingerprintsByStatus
class	FreeTextQuery select idchemical,metric from ( (select idchemical,2 as metric from properties join property_values using(idproperty) join property_string using(idvalue_string) join structure using(idstructure) where name like "MA%" and value like "Reaction%" ) union (select idchemical,2 as metric from properties join property_values using(idproperty) join property_string using(idvalue_string) join structure using(idstructure) where value like "MA%" and name like "Reaction%" ) union (select idchemical,1 as metric from properties join property_values using(idproperty) join structure using(idstructure) where name like "MA%") union (select idchemical,1 as metric from property_values join property_string using(idvalue_string) join structure using(idstructure) where value like "MA%") union (select idchemical,1 as metric from properties join property_values using(idproperty) join structure using(idstructure) where name like "Reaction%") union (select idchemical,1 as metric from property_values join property_string using(idvalue_string) join structure using(idstructure) where value like "Reaction%") ) a
class	MissingFingerprintsQuery
class	MissingInChIsQuery
class	NumberQuery<F>
class	QueryAtomEnvironment Similarity via atom environment matrix /query/similarity?search=c1ccccc1O&threshold=0.5&mode=ae
class	QueryByIdentifierWithStructureFallback Calls findByProperty stored procedure
class	QueryDataset src_dataset.name = ?
class	QueryDatasetByID
class	QueryDistance Distance between two atoms, provided as symbols.
class	QueryExactStructure Deprecated. Convert to InChI and use QueryStructure
class	QueryField Search for a structure with property with given name and value
class	QueryFieldAbstract<T,C extends net.idea.modbcum.i.IQueryCondition,NC extends net.idea.modbcum.i.IQueryCondition>
class	QueryFieldMultiple
class	QueryFieldNumeric
class	QueryFunctionalGroups
class	QueryLookupStructure This is a wrapper around QueryStructure , allowing to use IStructureRecord as a parameter
class	QueryMissingDescriptor reads structures, for each there are / or there are not (depending on getCondition) descriptors with given idname and reference title.
class	QueryMissingDistances Reads structures without precalculated pairwise atom distances from the database.
class	QueryMissingProperty
class	QueryPrescreenBitSet First bitset is from structural keys, second from fingerprints
class	QuerySimilarity<F,T,C extends net.idea.modbcum.i.IQueryCondition>
class	QuerySimilarityBitset Tanimoto similarity of BitSet.
class	QuerySimilarityStructure
class	QuerySMARTS Select structures by querying fungroups table by smarts
class	QueryStoredResults
class	QueryStoredResultsByName Retrieve structure collections from query table by name and folder (sessions table)
class	QueryStructure Search for smiles, inchi, formula
class	QueryStructureByID Selects a structure by idstructure
class	QueryStructureByQuality
class	QueryStructureByQualityPairLabel
class	QueryStructureByValueQuality
class	QueryStructureType
class	QueryStrucType
class	ScopeQuery A convenience class for a query used to restrict the scope of other queries

Uses of AbstractQuery in ambit2.db.search.structure.byproperty

Subclasses of AbstractQuery in ambit2.db.search.structure.byproperty

Modifier and Type	Class and Description
class	QueryStructureByProperty<Q extends AbstractStructureQuery>
class	QueryStructureByPropertyInCompounds
class	QueryStructureByPropertyInDataset
class	QueryStructuresByPropertyInResults

Uses of AbstractQuery in ambit2.db.search.structure.pairwise

Subclasses of AbstractQuery in ambit2.db.search.structure.pairwise

Modifier and Type	Class and Description
class	ChemicalSpaceQuery
class	QueryStructurePairs<Dataset1,Dataset2> returns idstructure of two molecules
class	QueryStructurePairsDataset Selects a structure by idstructure
class	QueryStructurePairsMixed
class	QueryStructurePairsRDataset
class	RetrieveStructurePair

Uses of AbstractQuery in ambit2.db.simiparity.space

Subclasses of AbstractQuery in ambit2.db.simiparity.space

Modifier and Type	Class and Description
class	QueryQMap Reads QMap
class	QueryQMapSpace Reads QMapSpace
class	QueryQMapStructures

Uses of AbstractQuery in ambit2.db.substance

Subclasses of AbstractQuery in ambit2.db.substance

Modifier and Type	Class and Description
class	AbstractReadSubstance<F,T>
class	FacetedSearchSubstance
class	ReadByReliabilityFlags
class	ReadSubstance
class	ReadSubstanceByExternalIDentifier
class	ReadSubstanceByName
class	ReadSubstanceByOwner All substance given an owner name or UUID
class	ReadSubstanceByStudy
class	ReadSubstanceByType
class	ReadSubstances Retrieve set of substances given array of substance UUIDs

Uses of AbstractQuery in ambit2.db.substance.ids

Subclasses of AbstractQuery in ambit2.db.substance.ids

Modifier and Type	Class and Description
class	ReadSubstanceIdentifiers

Uses of AbstractQuery in ambit2.db.substance.relation

Subclasses of AbstractQuery in ambit2.db.substance.relation

Modifier and Type	Class and Description
class	ChemicalBySubstanceRelation Returns all chemicals which are component of a substance.
class	ReadSubstanceComposition
class	ReadSubstanceRelation Reads all structures, related to the query substance via substance_relation table

Uses of AbstractQuery in ambit2.db.substance.study

Subclasses of AbstractQuery in ambit2.db.substance.study

Modifier and Type	Class and Description
class	ReadEffectRecord Reads effects records given document uuid
class	ReadEffectRecordAbstract<F,ER extends EffectRecord<String,String,String>>
class	ReadEffectRecordBySubstance
class	ReadSubstanceProperty
class	ReadSubstanceStudy<PA extends ProtocolApplication<Protocol,String,String,IParams,String>>

Uses of AbstractQuery in ambit2.db.update.bookmark

Subclasses of AbstractQuery in ambit2.db.update.bookmark

Modifier and Type	Class and Description
class	ReadAnnotation
class	ReadBookmark Bookmark

Uses of AbstractQuery in ambit2.db.update.bundle

Subclasses of AbstractQuery in ambit2.db.update.bundle

Modifier and Type	Class and Description
class	ReadBundle Retrieve SourceDataset by id
class	ReadBundleVersion

Uses of AbstractQuery in ambit2.db.update.bundle.chemicals

Subclasses of AbstractQuery in ambit2.db.update.bundle.chemicals

Modifier and Type	Class and Description
class	ReadChemicalsByBundle

Uses of AbstractQuery in ambit2.db.update.bundle.effects

Subclasses of AbstractQuery in ambit2.db.update.bundle.effects

Modifier and Type	Class and Description
class	ReadEffectRecordByBundle

Uses of AbstractQuery in ambit2.db.update.bundle.endpoints

Subclasses of AbstractQuery in ambit2.db.update.bundle.endpoints

Modifier and Type	Class and Description
class	ReadEndpointsByBundle

Uses of AbstractQuery in ambit2.db.update.bundle.matrix

Subclasses of AbstractQuery in ambit2.db.update.bundle.matrix

Modifier and Type	Class and Description
class	ReadEffectRecordByBundleMatrix

Uses of AbstractQuery in ambit2.db.update.bundle.substance

Subclasses of AbstractQuery in ambit2.db.update.bundle.substance

Modifier and Type	Class and Description
class	ReadSubstanceChemicalsUnionByBundle
class	ReadSubstancesByBundle
class	ReadSubstancesByBundleCompounds Retrieve substances, containing compounds defined by the /bundle/id/compound

Uses of AbstractQuery in ambit2.db.update.dataset

Subclasses of AbstractQuery in ambit2.db.update.dataset

Modifier and Type	Class and Description
class	AbstractReadDataset<T,M extends ISourceDataset>
class	DatasetQueryFieldGeneric<T,C extends net.idea.modbcum.i.IQueryCondition>
class	DatasetQueryFieldNumeric
class	DatasetQueryFieldString
class	QueryDatasetByFeatures
class	ReadDataset Retrieve SourceDataset by id
class	ReadDatasetLicense Retrieve SourceDataset by id

Uses of AbstractQuery in ambit2.db.update.fp

Subclasses of AbstractQuery in ambit2.db.update.fp

Modifier and Type	Class and Description
class	QueryFingerprints Expects 1024 bit fingerprint in the form of "0-0-0-0-0-20000000-0-0-0-0-0-0-0-0-0-10000000" (16x 64 bits)
class	ReadStructuresByFingerprint

Uses of AbstractQuery in ambit2.db.update.model

Subclasses of AbstractQuery in ambit2.db.update.model

Modifier and Type	Class and Description
class	AbstractModelQuery<F,V>
class	QueryModel
class	ReadModel ModelQueryResults

Uses of AbstractQuery in ambit2.db.update.property

Subclasses of AbstractQuery in ambit2.db.update.property

Modifier and Type	Class and Description
class	ReadProperty Reads Property by id

Uses of AbstractQuery in ambit2.db.update.propertyannotations

Subclasses of AbstractQuery in ambit2.db.update.propertyannotations

Modifier and Type	Class and Description
class	ReadPropertyAnnotations

Uses of AbstractQuery in ambit2.db.update.queryfolder

Subclasses of AbstractQuery in ambit2.db.update.queryfolder

Modifier and Type	Class and Description
class	ReadQueryFolder Retrieve query folder header by id or name

Uses of AbstractQuery in ambit2.db.update.reference

Subclasses of AbstractQuery in ambit2.db.update.reference

Modifier and Type	Class and Description
class	ReadReference Retrieve references (by id or all)

Uses of AbstractQuery in ambit2.db.update.storedquery

Subclasses of AbstractQuery in ambit2.db.update.storedquery

Modifier and Type	Class and Description
class	ReadStoredQuery
class	SearchStoredQueries

Uses of AbstractQuery in ambit2.db.update.structure

Subclasses of AbstractQuery in ambit2.db.update.structure

Modifier and Type	Class and Description
class	ChemicalByDataset idchemical by dataset

Uses of AbstractQuery in ambit2.db.version

Subclasses of AbstractQuery in ambit2.db.version

Modifier and Type	Class and Description
class	DBVersionQuery

Uses of AbstractQuery in ambit2.dbui

Classes in ambit2.dbui with type parameters of type AbstractQuery

Modifier and Type	Class and Description
class	QueryEditor<F,T,C extends net.idea.modbcum.i.IQueryCondition,ResultType,Q extends AbstractQuery<F,T,C,ResultType>>