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public interface ArrayDesignDataSource
Retrieves various MAGE objects needed to populate array designs.
Method Summary | |
---|---|
void |
addCompositeSequence(CompositeGroup compositeGroup,
CompositeSequence compositeSequence)
|
void |
create(PhysicalArrayDesign arrayDesign,
java.lang.String username)
Saves a new array design to the database. |
void |
disableIndexesAndConstraints()
Disables constraints and drops indexes in order to faster load array design data. |
void |
enableIndexesAndConstraints()
Re-enables constraints and adds indexes after array design loading. |
PhysicalArrayDesign[] |
getAllArrayDesigns()
Returns all array designs in the system |
PhysicalArrayDesign |
getArrayDesign(long id)
Returns the array design requested. |
PhysicalArrayDesign |
getArrayDesign(java.lang.String identifier)
Returns the existing array design matching the given identifier or null if none exists yet. |
ArrayDesignFileUploadEntry |
getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
Returns the upload entry associated with the array design, or null if there is none. |
OntologyEntry |
getOntologyEntry(java.lang.String category,
java.lang.String value)
Returns the entry corresponding to the data given or null if not found. |
Organization |
getOrganization(OrganizationDescriptor descriptor)
Returns the Organization corresponding to the descriptor given, creating if necessary. |
void |
makePublic(PhysicalArrayDesign arrayDesign,
java.lang.String username)
Makes an array design public. |
void |
removeExistingDesignElements(PhysicalArrayDesign newArrayDesign)
Clears all existing associated array design objects from the system, leaving only the top level PhysicalArrayDesign object. |
void |
save(PhysicalArrayDesign newArrayDesign)
Saves an existing array design to the database. |
DesignElementRetrievalSettings |
setEfficientDesignElementRetrieval()
Changes OJB auto-retrieval for design elements to false for all objects associated with design elements. |
void |
setNormalDesignElementRetrieval(DesignElementRetrievalSettings originalSettings)
Restores OJB design element auto-retrieve settings to their original values. |
Method Detail |
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OntologyEntry getOntologyEntry(java.lang.String category, java.lang.String value) throws ArrayDesignDataSourceException
category
- the categoryvalue
- the value
ArrayDesignDataSourceException
Organization getOrganization(OrganizationDescriptor descriptor) throws ArrayDesignDataSourceException
descriptor
- the organization's descriptor
ArrayDesignDataSourceException
void makePublic(PhysicalArrayDesign arrayDesign, java.lang.String username) throws ArrayDesignDataSourceException
arrayDesign
- the array design to make public.username
- the owner of the design.
ArrayDesignDataSourceException
void create(PhysicalArrayDesign arrayDesign, java.lang.String username) throws ArrayDesignDataSourceException
arrayDesign
- the array design to create.username
- the user creating the design.
ArrayDesignDataSourceException
PhysicalArrayDesign getArrayDesign(java.lang.String identifier) throws ArrayDesignDataSourceException
identifier
- identifier to match
ArrayDesignDataSourceException
PhysicalArrayDesign[] getAllArrayDesigns() throws ArrayDesignDataSourceException
ArrayDesignDataSourceException
void removeExistingDesignElements(PhysicalArrayDesign newArrayDesign) throws ArrayDesignDataSourceException
newArrayDesign
-
ArrayDesignDataSourceException
void save(PhysicalArrayDesign newArrayDesign) throws ArrayDesignDataSourceException
newArrayDesign
-
ArrayDesignDataSourceException
ArrayDesignFileUploadEntry getArrayDesignFileUploadEntry(PhysicalArrayDesign design) throws ArrayDesignDataSourceException
design
- get upload entry for this design
ArrayDesignDataSourceException
PhysicalArrayDesign getArrayDesign(long id) throws ArrayDesignDataSourceException
id
-
ArrayDesignDataSourceException
void disableIndexesAndConstraints() throws ArrayDesignDataSourceException
ArrayDesignDataSourceException
void enableIndexesAndConstraints() throws ArrayDesignDataSourceException
ArrayDesignDataSourceException
DesignElementRetrievalSettings setEfficientDesignElementRetrieval()
ArrayDesignDataSourceException
void setNormalDesignElementRetrieval(DesignElementRetrievalSettings originalSettings)
originalSettings
-
ArrayDesignDataSourceException
void addCompositeSequence(CompositeGroup compositeGroup, CompositeSequence compositeSequence)
compositeGroup
- compositeSequence
-
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