Uses of Class
uk.ac.cisban.rod.exception.QueryNotFoundException

Packages that use QueryNotFoundException

uk.ac.cisban.rod.dao	Database access package containing all code for database access.
uk.ac.cisban.rod.dao.specifics	Grouping specific sets of tasks together in communication to the database.
uk.ac.cisban.rod.data	Manages all data incoming from the database and forwards database requests from the GUI.
uk.ac.cisban.rod.data.handlers	Handles all of the connections with the DAO and keeps track of the progress of the task.

Uses of QueryNotFoundException in uk.ac.cisban.rod.dao

Methods in uk.ac.cisban.rod.dao that throw QueryNotFoundException

java.util.Map<java.lang.String,java.lang.Exception>	Persist.addPlateTreatments(java.util.List<java.lang.String> barcodes, java.util.Date date, java.lang.Long treatmentCvId)
java.util.Collection<PlateTreatment>	Persist.addPlateTreatments(java.lang.String barcode, java.util.ArrayList<java.util.Date> dates, java.util.ArrayList<java.lang.String> treatmentNames)
void	Delete.deleteLogs(Repeat r) Deletes from the database.
void	Delete.deleteMasterplateSet(MasterplateSet m) Deletes the MasterplateSet from the database.
void	Delete.deleteMasterplateSetAndPlates(MasterplateSet m) Deletes the MasterplateSet and associated Masterplates from the database.
ActionApplication	Find.findActionApplication(javax.jdo.PersistenceManager pm, long identifier) Finds a ActionApplication given its database id.
ActionCV	Find.findActionCV(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a ActionCV given its database id.
ActionCV	Find.findActionCV(javax.jdo.PersistenceManager pm, java.lang.String identifier) Finds an ActionCV given its XML identifier .
BackgroundMutationCV	Find.findBackgroundMutationCV(javax.jdo.PersistenceManager pm, java.lang.String mutationName) Finds a background mutation CV given its name.
Barcode	Find.findBarcode(javax.jdo.PersistenceManager pm, long id) Finds a Barcode given its database id .
Barcode	Find.findBarcode(javax.jdo.PersistenceManager pm, java.lang.String barcode) Finds a Barcode given its barcode String.
EquipmentCV	Find.findEquipmentCV(javax.jdo.PersistenceManager pm, java.lang.String identifier) Finds an EquipmentCV given its FuGE identifier.
Experiment	Find.findExperiment(javax.jdo.PersistenceManager pm, long id) Finds a Experiment given its database id.
Experiment	Find.findExperiment(javax.jdo.PersistenceManager pm, java.lang.String name) Finds a Experiment given its name.
FeatureCV	Find.findFeatureCV(javax.jdo.PersistenceManager pm, java.lang.String featureName) Finds a FeatureCV given its name.
Image	Find.findImage(javax.jdo.PersistenceManager pm, java.lang.String uri) Finds an Image given its URI.
ImageCV	Find.findImageCV(javax.jdo.PersistenceManager pm, java.lang.String description) Finds an ImageCV given its description.
java.util.Collection<Image>	Find.findImages(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId) Finds a collection of Images given their barcode database id .
java.util.Collection<ImageSpot>	Find.findImageSpot(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition) Finds a ImageSpot given its source PlatePosition database id.
ImageTransformationCV	Find.findImageTransformationCV(javax.jdo.PersistenceManager pm, java.lang.String name) Finds a ImageTransformationCV given its name.
Inoculation	Find.findInoculation(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition, java.lang.Long destinationPlatePosition) Finds a Inoculation given its source and destination PlatePosition DB ids.
java.util.Collection<Inoculation>	Find.findInoculationWithDestination(javax.jdo.PersistenceManager pm, java.lang.Long destinationPlatePosition) Finds a collection of Inoculations given their destination PlatePosition ids.
Masterplate	Find.findMasterplate(javax.jdo.PersistenceManager pm, java.lang.String barcode) Locates a Plate in the database, given a barcode String.
MasterplateLibraryCV	Find.findMasterplateLibraryCV(javax.jdo.PersistenceManager pm, java.lang.String name) Finds a MasterplateLibraryCV given its name.
MasterplatePosition	Find.findMasterplatePosition(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId, int row, int column) Finds a MasterplatePosition given its masterplate database id and row and column on the plate.
java.lang.Long	Exists.findMasterplatePositions(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId) Finds number of MasterplatePositions on a masterplate.
MasterplateSet	Find.findMasterplateSet(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a MasterplateSet given its database id .
MasterplateSet	Find.findMasterplateSet(javax.jdo.PersistenceManager pm, java.lang.String description) Finds a MasterplateSet given its description.
MediumCV	Find.findMediumCV(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a MediumCV given its database id .
MediumCV	Find.findMediumCV(javax.jdo.PersistenceManager pm, java.lang.String name) Finds a MediumCV given its name.
java.lang.String	Find.findORF(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId, java.lang.Long positionId) Finds an ORF given its masterplate database id and position database id.
Plate	Find.findPlate(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a Plate given its database id .
Plate	Find.findPlate(javax.jdo.PersistenceManager pm, java.lang.String barcode) Locates a Plate in the database, given a barcode String.
PlateCV	Find.findPlateCV(javax.jdo.PersistenceManager pm, long id) Finds a PlateCV given its database id .
PlateCV	Find.findPlateCV(javax.jdo.PersistenceManager pm, java.lang.String name) Finds a PlateCV given its name.
PlatePosition	Find.findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a PlatePosition given its DB id.
PlatePosition	Find.findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId, java.lang.Long positionId) Finds a PlatePosition given its Barcode and Position DB ids.
PlatePosition	Find.findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, int row, int column) Finds a PlatePosition given its Barcode value and row and column position.
PlatePosition	Find.findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, java.lang.Long positionId) Finds a PlatePosition given its Barcode value and Position DB id.
java.lang.Long	Exists.findPlatePositions(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId) Finds number of Spottings for a barcode DB id.
Position	Find.findPosition(javax.jdo.PersistenceManager pm, int row, int column) Finds a Position given its row and column.
ProtocolApplication	Find.findProtocolApplication(javax.jdo.PersistenceManager pm, long id) Finds a ProtocolApplication given its database id.
ProtocolCV	Find.findProtocolCV(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a ProtocolCV given its database id .
ProtocolCV	Find.findProtocolCV(javax.jdo.PersistenceManager pm, java.lang.String identifier) Finds a ProtocolCV given its database id.
Repeat	Find.findRepeat(javax.jdo.PersistenceManager pm, long id) Finds a Repeat given its database id.
protected java.util.Collection<Repeat>	Find.findRepeats(javax.jdo.PersistenceManager pm, Experiment exp) Gets all repeats for a given experiment using experiment id as an identifier.
protected java.util.Collection<Repeat>	Find.findRepeats(javax.jdo.PersistenceManager pm, long id) Gets all repeats for a given experiment using experiment id as an identifier.
ActionApplication	Find.findSpotLogs(javax.jdo.PersistenceManager pm, long actionApplicationId) Finds spot logs given an action application database id.
Spotting	Find.findSpotting(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition, java.lang.Long destinationPlatePosition) Finds a Spotting given its source and destination PlatePosition DB ids.
java.util.Collection<Spotting>	Find.findSpottingWithDestination(javax.jdo.PersistenceManager pm, java.lang.Long destinationPlatePosition) Finds a collection of Spottings given their destination PlatePosition DB id.
int	Find.findTimeseriesOrder(javax.jdo.PersistenceManager pm, Image image) Finds the number of an image part of a series of images taken of the same plate.
TreatmentCV	Find.findTreatmentCV(javax.jdo.PersistenceManager pm, java.lang.Long id) Finds a TreatmentCV given its database id .
TreatmentCV	Find.findTreatmentCV(javax.jdo.PersistenceManager pm, java.lang.String name) Finds a TreatmentCV given its name.
PlatePosition	Find.forceFindPlatePosition(javax.jdo.PersistenceManager pm, long barcodeId, int row, int column) Finds or creates a PlatePosition given its Barcode DB id and row and column.
PlatePosition	Find.forceFindPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, int row, int column) Finds or creates a PlatePosition given its Barcode value and row and column .
java.util.Collection<BackgroundMutationCV>	DAO.getBackgroundMutationCVs() Returns the whole list of BackgroundMutationCVs in the database.
java.util.Collection<Experiment>	DAO.getExperiments() Returns the whole list of Experiments in the database.
java.util.Collection<MasterplateLibraryCV>	DAO.getMasterplateLibraryCVs() Returns the whole list of MasterplateLibraryCVs in the database.
java.util.Collection<MasterplateSet>	DAO.getMasterplateSets() Returns the whole list of MasterplateSets in the database.
java.util.Collection<MediumCV>	DAO.getMediumCVs() Returns the whole list of MediumCVs in the database.
java.util.Collection<PlateCV>	DAO.getPlateCVs() Returns the whole list of PlateCVs in the database.
java.util.Collection<Plate>	DAO.getPlates() Returns the whole list of Plates in the database.
java.util.Collection<ProtocolCV>	DAO.getProtocols() Returns the whole list of ProtocolCVs in the database.
java.util.Collection<TreatmentCV>	DAO.getTreatmentCVs() Returns the whole list of TreatmentCVs in the database.
java.util.Collection<Image>	DAO.loadImagesBrief(java.util.List<java.lang.String> nonMappedPlates, java.lang.String barcodeString) Loads the collection of images associated with a Barcode without retrieving the individual ImageSpots (hence the "Brief").
java.util.Collection<LogEvent>	DAO.loadLogs(java.lang.Long actionAppId) Loads the LogEvents of an ActionApplication, given the AA's PK.
java.util.Collection<LogEventMapping>	DAO.loadSpots(java.util.Collection<java.lang.String> sourceBarcodes, long aAppId) Accesses the spot log for the given source barcodes based on ActionApplication id.
boolean	Find.mediumExists(javax.jdo.PersistenceManager pm, java.lang.String medName) Checks if a mediumCV exists.
ActionApplication	Persist.newActionApplication(java.lang.String actionRefId, java.lang.Long protocolAppId)
ActionCV	Persist.newActionCV(java.lang.String protocolID, java.lang.String identifier, int actionOrdinal, java.lang.String actionText, java.lang.String name, java.lang.String subProtocolID, boolean repeatable)
Experiment	Persist.newExperiment(java.lang.String name, java.lang.String description, java.lang.Long protocolCVId, boolean complete, java.lang.Long[] mpsSt)
Masterplate	Persist.newMasterplate(java.lang.String barcodeSt, java.util.Collection<MasterplatePosition> positions, java.lang.String mediumCVName, int plateno, java.util.Date datePoured, PlateCV plateCV)
MasterplateLibraryCV	Persist.newMasterplateLibraryCV(java.lang.String libraryName, long platecvId)
MasterplateLibraryCV	Persist.newMasterplateLibraryCV(java.lang.String libraryName, java.lang.String platecvName)
MasterplateSet	Persist.newMasterplateSet(java.util.Date date, java.lang.String description, java.lang.String librarySt, java.util.Set<java.lang.String> masterplateBarcodes, java.lang.String bgmutationcvSt)
Plate	Persist.newPlate(java.lang.String barcodeSt, java.lang.String mediumName, java.lang.String plateCVName, java.util.Date datePoured)
ProtocolApplication	Persist.newProtocolApplication(java.lang.Long protocolRefId, java.lang.String inputPlateCVId, java.lang.String outputPlateCVId)
ProtocolCV	Persist.newProtocolCV(java.lang.String identifier, java.lang.String name, java.util.Collection<java.lang.String> equipmentIds, boolean isShown)
Repeat	Persist.newRepeat(java.lang.String description, java.lang.String experimentSt, java.lang.String masterplateSetSt, java.lang.String protocolCVId)
Experiment	Persist.updateExperiment(java.lang.Long id, java.lang.String name, java.lang.String description, boolean complete)
MediumCV	Persist.updateMediumCV(java.lang.Long id, java.lang.String mediumName, java.lang.String description)
TreatmentCV	Persist.updateTreatmentCV(java.lang.Long id, java.lang.String name, java.lang.String description)

Uses of QueryNotFoundException in uk.ac.cisban.rod.dao.specifics

Methods in uk.ac.cisban.rod.dao.specifics that throw QueryNotFoundException

java.util.Collection<Image>	ManageLogs.loadImagesBrief(java.util.List<java.lang.String> nonMappedPlates, java.lang.String barcodeString) Loads the collection of images associated with a Barcode without retrieving the individual ImageSpots (hence the "Brief").
java.util.Collection<LogEvent>	ManageLogs.loadLogs(java.lang.Long actionAppId) Loads the LogEvents of an ActionApplication, given the AA's PK.
java.util.Collection<LogEventMapping>	ManageLogs.loadSpots(java.util.Collection<java.lang.String> sourceBarcodes, long aAppId) Accesses the spot log for the given source barcodes based on ActionApplication id.
void	Export.printImageSpot(javax.jdo.PersistenceManager pm, Image image, long numSpots, Repeat repeat, ImageSpot imageSpot) Gathers up all of the information for the ROD export file, sticks it in a CompleteQueryResult, and then sends it to the printer for printing.

Uses of QueryNotFoundException in uk.ac.cisban.rod.data

Methods in uk.ac.cisban.rod.data that throw QueryNotFoundException

java.util.Collection<BackgroundMutationCV>	PlateManager.getBackgroundMutationCVs() creates a link to the database and retrieves all backgroundMutationCVs.
java.util.Collection<Experiment>	ExperimentManager.getExperiments() Retrieves all experiments from the database.
java.util.Collection<MasterplateLibraryCV>	PlateManager.getMasterplateLibraryCVs() creates a link to the database and retrieves all MasterplatelibraryCVs.
java.util.Collection<MasterplateSet>	PlateManager.getMasterplateSets() creates a link to the database and retrieves all masterplates sets.
java.util.Collection<MediumCV>	PlateManager.getMediumCVs() creates a link to the database and retrieves all mediumCVs.
java.util.Collection<PlateCV>	PlateManager.getPlateCVs() creates a link to the database and retrieves all plateCVs.
java.util.Collection<Plate>	PlateManager.getPlates() creates a link to the database and retrieves all plates.
java.util.Collection<ProtocolCV>	ExperimentManager.getProtocols() Retrieves all protocols from the database.
java.util.Collection<TreatmentCV>	PlateManager.getTreatmentCVs() creates a link to the database and retrieves all treatments.

Uses of QueryNotFoundException in uk.ac.cisban.rod.data.handlers

Methods in uk.ac.cisban.rod.data.handlers that throw QueryNotFoundException

java.lang.Void	AddRepeatTask.doInBackground() connects to database and adds a new background mutation cv
Experiment	NewExperimentTask.newExperiment(Experiment screen)