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java.lang.Object uk.ac.cisban.rod.dao.Find
public class Find
For checking for and retrieving objects in the database.
Constructor Summary | |
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Find(DAO dao)
Even though DAO is a singleton, we pass to the constructor to avoid an infinite recursion. |
Method Summary | |
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java.util.Map<java.lang.String,java.lang.Exception> |
fillPlateList(javax.jdo.PersistenceManager pm,
java.util.List<java.lang.String> barcodes,
java.util.List<Plate> listToFill)
Fills the given list using the given barcodes with Plates from the DB. |
ActionApplication |
findActionApplication(javax.jdo.PersistenceManager pm,
long identifier)
Finds a ActionApplication given its database id. |
ActionCV |
findActionCV(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a ActionCV given its database id. |
ActionCV |
findActionCV(javax.jdo.PersistenceManager pm,
java.lang.String identifier)
Finds an ActionCV given its XML identifier . |
BackgroundMutationCV |
findBackgroundMutationCV(javax.jdo.PersistenceManager pm,
java.lang.String mutationName)
Finds a background mutation CV given its name. |
Barcode |
findBarcode(javax.jdo.PersistenceManager pm,
long id)
Finds a Barcode given its database id . |
Barcode |
findBarcode(javax.jdo.PersistenceManager pm,
java.lang.String barcode)
Finds a Barcode given its barcode String. |
EquipmentCV |
findEquipmentCV(javax.jdo.PersistenceManager pm,
java.lang.String identifier)
Finds an EquipmentCV given its FuGE identifier. |
Experiment |
findExperiment(javax.jdo.PersistenceManager pm,
long id)
Finds a Experiment given its database id. |
Experiment |
findExperiment(javax.jdo.PersistenceManager pm,
java.lang.String name)
Finds a Experiment given its name. |
FeatureCV |
findFeatureCV(javax.jdo.PersistenceManager pm,
java.lang.String featureName)
Finds a FeatureCV given its name. |
Image |
findImage(javax.jdo.PersistenceManager pm,
java.lang.String uri)
Finds an Image given its URI. |
ImageCV |
findImageCV(javax.jdo.PersistenceManager pm,
java.lang.String description)
Finds an ImageCV given its description. |
java.util.Collection<Image> |
findImages(javax.jdo.PersistenceManager pm,
java.lang.Long barcodeId)
Finds a collection of Images given their barcode database id . |
java.util.Collection<ImageSpot> |
findImageSpot(javax.jdo.PersistenceManager pm,
java.lang.Long sourcePlatePosition)
Finds a ImageSpot given its source PlatePosition database id. |
ImageTransformationCV |
findImageTransformationCV(javax.jdo.PersistenceManager pm,
java.lang.String name)
Finds a ImageTransformationCV given its name. |
Inoculation |
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> |
findInoculationWithDestination(javax.jdo.PersistenceManager pm,
java.lang.Long destinationPlatePosition)
Finds a collection of Inoculations given their destination PlatePosition ids. |
Masterplate |
findMasterplate(javax.jdo.PersistenceManager pm,
java.lang.String barcode)
Locates a Plate in the database, given a barcode String. |
MasterplateLibraryCV |
findMasterplateLibraryCV(javax.jdo.PersistenceManager pm,
java.lang.String name)
Finds a MasterplateLibraryCV given its name. |
MasterplatePosition |
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. |
MasterplateSet |
findMasterplateSet(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a MasterplateSet given its database id . |
MasterplateSet |
findMasterplateSet(javax.jdo.PersistenceManager pm,
java.lang.String description)
Finds a MasterplateSet given its description. |
MediumCV |
findMediumCV(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a MediumCV given its database id . |
MediumCV |
findMediumCV(javax.jdo.PersistenceManager pm,
java.lang.String name)
Finds a MediumCV given its name. |
java.lang.String |
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 |
findPlate(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a Plate given its database id . |
Plate |
findPlate(javax.jdo.PersistenceManager pm,
java.lang.String barcode)
Locates a Plate in the database, given a barcode String. |
PlateCV |
findPlateCV(javax.jdo.PersistenceManager pm,
long id)
Finds a PlateCV given its database id . |
PlateCV |
findPlateCV(javax.jdo.PersistenceManager pm,
java.lang.String name)
Finds a PlateCV given its name. |
PlatePosition |
findPlatePosition(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a PlatePosition given its DB id. |
PlatePosition |
findPlatePosition(javax.jdo.PersistenceManager pm,
java.lang.Long barcodeId,
java.lang.Long positionId)
Finds a PlatePosition given its Barcode and Position DB ids. |
PlatePosition |
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 |
findPlatePosition(javax.jdo.PersistenceManager pm,
java.lang.String barcode,
java.lang.Long positionId)
Finds a PlatePosition given its Barcode value and Position DB id. |
Position |
findPosition(javax.jdo.PersistenceManager pm,
int row,
int column)
Finds a Position given its row and column. |
ProtocolApplication |
findProtocolApplication(javax.jdo.PersistenceManager pm,
long id)
Finds a ProtocolApplication given its database id. |
ProtocolCV |
findProtocolCV(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a ProtocolCV given its database id . |
ProtocolCV |
findProtocolCV(javax.jdo.PersistenceManager pm,
java.lang.String identifier)
Finds a ProtocolCV given its database id. |
Repeat |
findRepeat(javax.jdo.PersistenceManager pm,
long id)
Finds a Repeat given its database id. |
protected java.util.Collection<Repeat> |
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> |
findRepeats(javax.jdo.PersistenceManager pm,
long id)
Gets all repeats for a given experiment using experiment id as an identifier. |
ActionApplication |
findSpotLogs(javax.jdo.PersistenceManager pm,
long actionApplicationId)
Finds spot logs given an action application database id. |
Spotting |
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> |
findSpottingWithDestination(javax.jdo.PersistenceManager pm,
java.lang.Long destinationPlatePosition)
Finds a collection of Spottings given their destination PlatePosition DB id. |
int |
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 |
findTreatmentCV(javax.jdo.PersistenceManager pm,
java.lang.Long id)
Finds a TreatmentCV given its database id . |
TreatmentCV |
findTreatmentCV(javax.jdo.PersistenceManager pm,
java.lang.String name)
Finds a TreatmentCV given its name. |
PlatePosition |
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 |
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 . |
Position |
forceFindPosition(javax.jdo.PersistenceManager pm,
int row,
int column)
Finds a Position given its row and column. |
boolean |
mediumExists(javax.jdo.PersistenceManager pm,
java.lang.String medName)
Checks if a mediumCV exists. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Find(DAO dao)
dao
- the database access object.Method Detail |
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public int findTimeseriesOrder(javax.jdo.PersistenceManager pm, Image image) throws QueryNotFoundException
pm
- persistence managerimage
- the image to find the timeseries order or
QueryNotFoundException
- if there are no images of the barcoded platepublic BackgroundMutationCV findBackgroundMutationCV(javax.jdo.PersistenceManager pm, java.lang.String mutationName) throws QueryNotFoundException
pm
- the persistence managermutationName
-
QueryNotFoundException
public FeatureCV findFeatureCV(javax.jdo.PersistenceManager pm, java.lang.String featureName) throws QueryNotFoundException
pm
- the persistence managerfeatureName
- the name
QueryNotFoundException
public Image findImage(javax.jdo.PersistenceManager pm, java.lang.String uri) throws QueryNotFoundException
pm
- the persistence manageruri
- the URI of the image
QueryNotFoundException
public java.util.Collection<Image> findImages(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId) throws QueryNotFoundException
pm
- the persistence managerbarcodeId
- the database id of the barcode
QueryNotFoundException
public ImageCV findImageCV(javax.jdo.PersistenceManager pm, java.lang.String description) throws QueryNotFoundException
pm
- the persistence managerdescription
- the description
QueryNotFoundException
public ImageTransformationCV findImageTransformationCV(javax.jdo.PersistenceManager pm, java.lang.String name) throws QueryNotFoundException
pm
- the persistence managername
- the name
QueryNotFoundException
public MasterplateLibraryCV findMasterplateLibraryCV(javax.jdo.PersistenceManager pm, java.lang.String name) throws QueryNotFoundException
pm
- the persistence managername
- the name
QueryNotFoundException
public MediumCV findMediumCV(javax.jdo.PersistenceManager pm, java.lang.String name) throws QueryNotFoundException
pm
- the persistence managername
- the name
QueryNotFoundException
public MediumCV findMediumCV(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id
QueryNotFoundException
public boolean mediumExists(javax.jdo.PersistenceManager pm, java.lang.String medName) throws QueryNotFoundException
pm
- instance of a performance managermedName
- name of medium to locate
QueryNotFoundException
- thrown if medium not found so returns false.public PlateCV findPlateCV(javax.jdo.PersistenceManager pm, java.lang.String name) throws QueryNotFoundException
pm
- the persistence managername
- the name
QueryNotFoundException
public PlateCV findPlateCV(javax.jdo.PersistenceManager pm, long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id
QueryNotFoundException
public TreatmentCV findTreatmentCV(javax.jdo.PersistenceManager pm, java.lang.String name) throws QueryNotFoundException
pm
- the persistence managername
- the name
QueryNotFoundException
public TreatmentCV findTreatmentCV(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the TreatmentCV
QueryNotFoundException
public Barcode findBarcode(javax.jdo.PersistenceManager pm, long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the Barcode
QueryNotFoundException
public Barcode findBarcode(javax.jdo.PersistenceManager pm, java.lang.String barcode) throws QueryNotFoundException
pm
- the persistence managerbarcode
- the Barcode value
QueryNotFoundException
public Plate findPlate(javax.jdo.PersistenceManager pm, java.lang.String barcode) throws QueryNotFoundException
pm
- the persistence managerbarcode
- the String identifier of the barcode
QueryNotFoundException
- if either the Plate or the Barcode can't be foundpublic Masterplate findMasterplate(javax.jdo.PersistenceManager pm, java.lang.String barcode) throws QueryNotFoundException
pm
- the persistence managerbarcode
- the String identifier of the barcode
QueryNotFoundException
- if either the Plate or the Barcode can't be foundpublic java.lang.String findORF(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId, java.lang.Long positionId) throws QueryNotFoundException
pm
- the persistence managermasterplateId
- positionId
-
QueryNotFoundException
public MasterplatePosition findMasterplatePosition(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId, int row, int column) throws QueryNotFoundException
pm
- the persistence managermasterplateId
- row
- column
-
QueryNotFoundException
public Plate findPlate(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the Plate
QueryNotFoundException
public EquipmentCV findEquipmentCV(javax.jdo.PersistenceManager pm, java.lang.String identifier) throws QueryNotFoundException
pm
- the persistence manageridentifier
- the FuGE identifier of the EquipmentCV
QueryNotFoundException
public MasterplateSet findMasterplateSet(javax.jdo.PersistenceManager pm, java.lang.String description) throws QueryNotFoundException
pm
- the persistence managerdescription
- the description of the MasterplateSet
QueryNotFoundException
public MasterplateSet findMasterplateSet(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the MasterplateSet
QueryNotFoundException
public ProtocolCV findProtocolCV(javax.jdo.PersistenceManager pm, java.lang.String identifier) throws QueryNotFoundException
pm
- the persistence manageridentifier
- the database id of the ProtocolCV
QueryNotFoundException
public ProtocolCV findProtocolCV(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the ProtocolCV
QueryNotFoundException
public ProtocolApplication findProtocolApplication(javax.jdo.PersistenceManager pm, long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the ProtocolApplication
QueryNotFoundException
public ActionCV findActionCV(javax.jdo.PersistenceManager pm, java.lang.String identifier) throws QueryNotFoundException
pm
- the persistence manageridentifier
- the XML identifier of the ActionCV
QueryNotFoundException
public ActionCV findActionCV(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
-
QueryNotFoundException
public ActionApplication findActionApplication(javax.jdo.PersistenceManager pm, long identifier) throws QueryNotFoundException
pm
- the persistence manageridentifier
- the database id of the ActionApplication
QueryNotFoundException
public ActionApplication findSpotLogs(javax.jdo.PersistenceManager pm, long actionApplicationId) throws QueryNotFoundException
pm
- the persistence manageractionApplicationId
-
QueryNotFoundException
public Experiment findExperiment(javax.jdo.PersistenceManager pm, java.lang.String name) throws QueryNotFoundException
pm
- the persistence managername
- the name of the Experiment
QueryNotFoundException
public Experiment findExperiment(javax.jdo.PersistenceManager pm, long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the Experiment
QueryNotFoundException
public Repeat findRepeat(javax.jdo.PersistenceManager pm, long id) throws QueryNotFoundException
pm
- the persistence managerid
- the database id of the Repeat
QueryNotFoundException
protected java.util.Collection<Repeat> findRepeats(javax.jdo.PersistenceManager pm, long id) throws QueryNotFoundException
pm
- the persistence managerid
- Experiments id.
QueryNotFoundException
protected java.util.Collection<Repeat> findRepeats(javax.jdo.PersistenceManager pm, Experiment exp) throws QueryNotFoundException
pm
- the persistence managerexp
- Experiment to get the repeats of.
QueryNotFoundException
public Inoculation findInoculation(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition, java.lang.Long destinationPlatePosition) throws QueryNotFoundException
PlatePosition
DB ids.
pm
- the persistence managersourcePlatePosition
- destinationPlatePosition
-
QueryNotFoundException
public java.util.Collection<Inoculation> findInoculationWithDestination(javax.jdo.PersistenceManager pm, java.lang.Long destinationPlatePosition) throws QueryNotFoundException
PlatePosition
ids.
pm
- the persistence managerdestinationPlatePosition
-
QueryNotFoundException
public Spotting findSpotting(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition, java.lang.Long destinationPlatePosition) throws QueryNotFoundException
PlatePosition
DB ids.
pm
- the persistence managersourcePlatePosition
- the of the SpottingdestinationPlatePosition
- the of the Spotting
QueryNotFoundException
public java.util.Collection<Spotting> findSpottingWithDestination(javax.jdo.PersistenceManager pm, java.lang.Long destinationPlatePosition) throws QueryNotFoundException
PlatePosition
DB id.
pm
- the persistence managerdestinationPlatePosition
- the of the Spottings
QueryNotFoundException
public java.util.Collection<ImageSpot> findImageSpot(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition) throws QueryNotFoundException
pm
- the persistence managersourcePlatePosition
- the database id of the source plate position
QueryNotFoundException
public Position findPosition(javax.jdo.PersistenceManager pm, int row, int column) throws QueryNotFoundException
pm
- the persistence managerrow
- column
-
QueryNotFoundException
public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, java.lang.Long positionId) throws QueryNotFoundException
Barcode
value and Position
DB id.
pm
- the persistence managerbarcode
- positionId
-
QueryNotFoundException
public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, int row, int column) throws QueryNotFoundException
Barcode
value and row and column position.
pm
- the persistence managerbarcode
- the barcode of the platerow
- the row of the positioncolumn
- the column of the position
QueryNotFoundException
public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId, java.lang.Long positionId) throws QueryNotFoundException
Barcode
and Position
DB ids.
pm
- the persistence managerbarcodeId
- the of the PlatePositionpositionId
- the of the PlatePosition
QueryNotFoundException
public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.Long id) throws QueryNotFoundException
pm
- the persistence managerid
-
QueryNotFoundException
public Position forceFindPosition(javax.jdo.PersistenceManager pm, int row, int column)
pm
- the persistence managerrow
- column
-
public PlatePosition forceFindPlatePosition(javax.jdo.PersistenceManager pm, long barcodeId, int row, int column) throws QueryNotFoundException
Barcode
DB id and row and column.
pm
- the persistence managerbarcodeId
- the of the PlatePositionrow
- the of the PlatePositioncolumn
- the of the PlatePosition
QueryNotFoundException
public PlatePosition forceFindPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, int row, int column) throws QueryNotFoundException
Barcode
value and row and column .
pm
- the persistence managerbarcode
- the of the PlatePositionrow
- the of the PlatePositioncolumn
- the of the PlatePosition
QueryNotFoundException
public java.util.Map<java.lang.String,java.lang.Exception> fillPlateList(javax.jdo.PersistenceManager pm, java.util.List<java.lang.String> barcodes, java.util.List<Plate> listToFill)
pm
- the persistence managerbarcodes
- the barcodes of the plateslistToFill
- the list to fill with Plates
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PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |