Uses of Class
org.biomage.ArrayDesign.PhysicalArrayDesign

Packages that use PhysicalArrayDesign
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
 

Methods in gov.nih.nci.caarray.services.arraydesign that return PhysicalArrayDesign
 PhysicalArrayDesign ArrayDesignManager.createArrayDesign(ArrayDesignType type, java.lang.String arrayDesignName, java.lang.String currentUsername)
          Creates a new array design.
 PhysicalArrayDesign[] DbArrayDesignDataSource.getAllArrayDesigns()
           
 PhysicalArrayDesign[] ArrayDesignDataSource.getAllArrayDesigns()
          Returns all array designs in the system
 PhysicalArrayDesign DbArrayDesignDataSource.getArrayDesign(long id)
           
 PhysicalArrayDesign ArrayDesignManagerDB.getArrayDesign(long id)
           
 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)
           
 PhysicalArrayDesign ArrayDesignManagerDB.getArrayDesign(java.lang.String identifier)
           
 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
 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)
           
 void DbArrayDesignDataSource.create(PhysicalArrayDesign arrayDesign, java.lang.String username)
           
 void ArrayDesignDataSource.create(PhysicalArrayDesign arrayDesign, java.lang.String username)
          Saves a new array design to the database.
 ArrayDesignFileUploadEntry DbArrayDesignDataSource.getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
           
 ArrayDesignFileUploadEntry ArrayDesignManagerDB.getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
           
 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)
           
 void CaArrayArrayDesignSecurityHelper.makePublic(PhysicalArrayDesign arrayDesign, java.lang.String ownerUsername)
           
 void ArrayDesignSecurityHelper.makePublic(PhysicalArrayDesign arrayDesign, java.lang.String ownerUsername)
           
 void ArrayDesignDataSource.makePublic(PhysicalArrayDesign arrayDesign, java.lang.String username)
          Makes an array design public.
 void DbArrayDesignDataSource.removeExistingDesignElements(PhysicalArrayDesign arrayDesign)
           
 void ArrayDesignManagerDB.removeExistingDesignElements(PhysicalArrayDesign arrayDesign)
           
 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)
           
 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)
           
 void ArrayDesignManagerDB.updateTopLevelOnly(PhysicalArrayDesign arrayDesign)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader with parameters of type PhysicalArrayDesign
static void ArrayDesignCleaner.removeDesignElements(PhysicalArrayDesign design)
           
 void ArrayDesignSaver.saveTopLevelElements(PhysicalArrayDesign arrayDesign)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.affymetrix
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader.affymetrix with parameters of type PhysicalArrayDesign
 void AffymetrixArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.agilent
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader.agilent that return PhysicalArrayDesign
 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
 void AgilentTxtArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.genepix
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader.genepix that return PhysicalArrayDesign
 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
 void GenepixGprArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 void GenepixGalArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.illumina
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader.illumina with parameters of type PhysicalArrayDesign
 void IlluminaArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.imagene
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader.imagene that return PhysicalArrayDesign
 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
 void ImageneTxtArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.arraydesign.loader.ucsf
 

Methods in gov.nih.nci.caarray.services.arraydesign.loader.ucsf that return PhysicalArrayDesign
 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
 void UcsfGprArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 void UcsfGalArrayDesignLoader.reloadArrayDesign(PhysicalArrayDesign design)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.experiment
 

Methods in gov.nih.nci.caarray.services.experiment that return PhysicalArrayDesign
 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
 

Methods in gov.nih.nci.caarray.services.fileparse.gal.magemapping that return PhysicalArrayDesign
 PhysicalArrayDesign GalToMageMapping.getGalToMageMapping(ArrayDesignDesc arrayDesignDesc, GalBlockData[] galBlocks, GalFeatureData[] featureData)
           
 

Uses of PhysicalArrayDesign in gov.nih.nci.caarray.services.fileupload2
 

Methods in gov.nih.nci.caarray.services.fileupload2 that return PhysicalArrayDesign
 PhysicalArrayDesign ArrayDesignFileUploadEntry.getArrayDesign()
           
 

Methods in gov.nih.nci.caarray.services.fileupload2 with parameters of type PhysicalArrayDesign
 void ArrayDesignFileUploadEntry.setArrayDesign(PhysicalArrayDesign arrayDesign)