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Packages that use PhysicalArrayDesign | |
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gov.nih.nci.caarray.services.arraydesign | |
gov.nih.nci.caarray.services.arraydesign.loader | |
gov.nih.nci.caarray.services.arraydesign.loader.affymetrix | |
gov.nih.nci.caarray.services.arraydesign.loader.agilent | |
gov.nih.nci.caarray.services.arraydesign.loader.genepix | |
gov.nih.nci.caarray.services.arraydesign.loader.illumina | |
gov.nih.nci.caarray.services.arraydesign.loader.imagene | |
gov.nih.nci.caarray.services.arraydesign.loader.ucsf | |
gov.nih.nci.caarray.services.experiment | |
gov.nih.nci.caarray.services.fileparse.gal.magemapping | |
gov.nih.nci.caarray.services.fileupload2 | This package provides supporting persistable beans for managing hybridization and array design file upload and parsing processes... |
Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign |
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Methods in gov.nih.nci.caarray.services.arraydesign that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
ArrayDesignManager.createArrayDesign(ArrayDesignType type,
java.lang.String arrayDesignName,
java.lang.String currentUsername)
Creates a new array design. |
PhysicalArrayDesign[] |
DbArrayDesignDataSource.getAllArrayDesigns()
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PhysicalArrayDesign[] |
ArrayDesignDataSource.getAllArrayDesigns()
Returns all array designs in the system |
PhysicalArrayDesign |
DbArrayDesignDataSource.getArrayDesign(long id)
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PhysicalArrayDesign |
ArrayDesignManagerDB.getArrayDesign(long id)
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PhysicalArrayDesign |
ArrayDesignManager.getArrayDesign(long arrayDesignId)
Returns the array design matching the given id. |
PhysicalArrayDesign |
ArrayDesignDataSource.getArrayDesign(long id)
Returns the array design requested. |
PhysicalArrayDesign |
DbArrayDesignDataSource.getArrayDesign(java.lang.String identifier)
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PhysicalArrayDesign |
ArrayDesignManagerDB.getArrayDesign(java.lang.String identifier)
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PhysicalArrayDesign |
ArrayDesignManager.getArrayDesign(java.lang.String identifier)
Returns the requested array design. |
PhysicalArrayDesign |
ArrayDesignDataSource.getArrayDesign(java.lang.String identifier)
Returns the existing array design matching the given identifier or null if none exists yet. |
PhysicalArrayDesign[] |
ArrayDesignManagerDB.getArrayDesigns(ArrayDesignSearchCriteria searchCriteria)
Get an array of ArrayDesign that match the specified
Criteria and that the array design is NOT marked as deleted. |
Methods in gov.nih.nci.caarray.services.arraydesign with parameters of type PhysicalArrayDesign | |
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long |
ArrayDesignManagerDB.addArrayDesign(PhysicalArrayDesign arrayDesign)
Adds the specified ArrayDesign to the persistence store |
static void |
ArrayDesignUtils.copy(ArrayDesignData source,
PhysicalArrayDesign target)
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types. |
static void |
ArrayDesignUtils.copy(PhysicalArrayDesign source,
ArrayDesignData target)
Copy data from the source to the target object based on the mapping instructions tagged in the source and target object types. |
static void |
ArrayDesignUtils.copy(PhysicalArrayDesign source,
ArrayDesignDesc target)
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void |
DbArrayDesignDataSource.create(PhysicalArrayDesign arrayDesign,
java.lang.String username)
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void |
ArrayDesignDataSource.create(PhysicalArrayDesign arrayDesign,
java.lang.String username)
Saves a new array design to the database. |
ArrayDesignFileUploadEntry |
DbArrayDesignDataSource.getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
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ArrayDesignFileUploadEntry |
ArrayDesignManagerDB.getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
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ArrayDesignFileUploadEntry |
ArrayDesignDataSource.getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
Returns the upload entry associated with the array design, or null if there is none. |
void |
DbArrayDesignDataSource.makePublic(PhysicalArrayDesign arrayDesign,
java.lang.String username)
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void |
CaArrayArrayDesignSecurityHelper.makePublic(PhysicalArrayDesign arrayDesign,
java.lang.String ownerUsername)
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void |
ArrayDesignSecurityHelper.makePublic(PhysicalArrayDesign arrayDesign,
java.lang.String ownerUsername)
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void |
ArrayDesignDataSource.makePublic(PhysicalArrayDesign arrayDesign,
java.lang.String username)
Makes an array design public. |
void |
DbArrayDesignDataSource.removeExistingDesignElements(PhysicalArrayDesign arrayDesign)
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void |
ArrayDesignManagerDB.removeExistingDesignElements(PhysicalArrayDesign arrayDesign)
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void |
ArrayDesignDataSource.removeExistingDesignElements(PhysicalArrayDesign newArrayDesign)
Clears all existing associated array design objects from the system, leaving only the top level PhysicalArrayDesign object. |
void |
DbArrayDesignDataSource.save(PhysicalArrayDesign arrayDesign)
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void |
ArrayDesignManager.save(PhysicalArrayDesign arrayDesign)
Stores the given array design to the database. |
void |
ArrayDesignDataSource.save(PhysicalArrayDesign newArrayDesign)
Saves an existing array design to the database. |
void |
ArrayDesignManagerDB.saveArrayDesign(PhysicalArrayDesign arrayDesign)
Alternate (to addArrayDesign) method for saving an array design -- assumes that the associated OntologyEntries are correct and stores all associated objects automatically. |
void |
ArrayDesignManagerDB.updateArrayDesign(PhysicalArrayDesign arrayDesign)
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void |
ArrayDesignManagerDB.updateTopLevelOnly(PhysicalArrayDesign arrayDesign)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader with parameters of type PhysicalArrayDesign | |
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static void |
ArrayDesignCleaner.removeDesignElements(PhysicalArrayDesign design)
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void |
ArrayDesignSaver.saveTopLevelElements(PhysicalArrayDesign arrayDesign)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.affymetrix |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader.affymetrix with parameters of type PhysicalArrayDesign | |
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void |
AffymetrixArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.agilent |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader.agilent that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
AgilentTxtArrayDesignLoader.getArrayDesign()
Creates and returns the array design object from the .TXT file. |
Methods in gov.nih.nci.caarray.services.arraydesign.loader.agilent with parameters of type PhysicalArrayDesign | |
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void |
AgilentTxtArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.genepix |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader.genepix that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
GenepixGprArrayDesignLoader.getArrayDesign()
Creates and returns the array design object from the .CDF file. |
PhysicalArrayDesign |
GenepixGalArrayDesignLoader.getArrayDesign()
Creates and returns the array design object from the .CDF file. |
Methods in gov.nih.nci.caarray.services.arraydesign.loader.genepix with parameters of type PhysicalArrayDesign | |
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void |
GenepixGprArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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void |
GenepixGalArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.illumina |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader.illumina with parameters of type PhysicalArrayDesign | |
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void |
IlluminaArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.imagene |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader.imagene that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
ImageneTxtArrayDesignLoader.getArrayDesign()
Creates and returns the array design object from the .TXT file. |
Methods in gov.nih.nci.caarray.services.arraydesign.loader.imagene with parameters of type PhysicalArrayDesign | |
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void |
ImageneTxtArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.ucsf |
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Methods in gov.nih.nci.caarray.services.arraydesign.loader.ucsf that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
UcsfGprArrayDesignLoader.getArrayDesign()
Creates and returns the array design object from the .CDF file. |
PhysicalArrayDesign |
UcsfGalArrayDesignLoader.getArrayDesign()
Creates and returns the array design object from the .CDF file. |
Methods in gov.nih.nci.caarray.services.arraydesign.loader.ucsf with parameters of type PhysicalArrayDesign | |
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void |
UcsfGprArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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void |
UcsfGalArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.experiment |
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Methods in gov.nih.nci.caarray.services.experiment that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
ExperimentManagerDB.getArrayDesign(long id)
This method returns a PhysicalArrayDesign that has the specified
ID by delegating the call to the same method in ArrayDesignManagerDB . |
Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.fileparse.gal.magemapping |
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Methods in gov.nih.nci.caarray.services.fileparse.gal.magemapping that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
GalToMageMapping.getGalToMageMapping(ArrayDesignDesc arrayDesignDesc,
GalBlockData[] galBlocks,
GalFeatureData[] featureData)
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Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.fileupload2 |
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Methods in gov.nih.nci.caarray.services.fileupload2 that return PhysicalArrayDesign | |
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PhysicalArrayDesign |
ArrayDesignFileUploadEntry.getArrayDesign()
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Methods in gov.nih.nci.caarray.services.fileupload2 with parameters of type PhysicalArrayDesign | |
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void |
ArrayDesignFileUploadEntry.setArrayDesign(PhysicalArrayDesign arrayDesign)
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