public class DataFileType extends BasicItem<DataFileTypeData> implements Nameable, Removable, ToTransferable<DataFileTypeInfo>, Validatable
Modifier and Type | Field and Description |
---|---|
static String |
AFFYMETRIX_CDF
The external ID for the file type representing
Affymetrix CDF files.
|
static String |
AFFYMETRIX_CEL
The external ID for the file type representing
Affymetrix CEL files.
|
static String |
BAM
The external ID for the file type representing
a BAM (Binary Sequence Alignment/Map) file.
|
static String |
BASEFILE_MATRIX
The external ID for the file type representing
a matrix BASEFile.
|
static String |
BASEFILE_SERIAL
The external ID for the file type representing
a serial BASEFile.
|
static String |
BFS_METADATA
The external ID for the file type representing a BFS
metadata file.
|
static String |
FPKM_TRACKING
The external ID for the file type representing a FPKM
tracking file.
|
static String |
GENERIC_EXTRAVALUE_DATA
The external ID for the file type representing
generic analysed extra value data.
|
static String |
GENERIC_PRINT_MAP
The external ID for the file type representing
a generic print map (array design layout) of any type.
|
static String |
GENERIC_RAW_DATA
The external ID for the file type representing
a generic raw data file of any type.
|
static String |
GENERIC_REPORTER_MAP
The external ID for the file type representing
a generic reporter map (array design layout) of any type.
|
static String |
GENERIC_SPOT_DATA
The external ID for the file type representing
generic analysed spot data.
|
static int |
MAX_EXTENSION_LENGTH
The maximum length of the file extension that can be stored in the database.
|
static int |
MAX_EXTERNAL_ID_LENGTH
The maximum length of the external ID that can be stored in the database.
|
static String |
MEV_TDMS
The external ID for the file type representing
a MeV TDMS (Tab-Delimited Multiple Sample) file.
|
static String |
MICROARRAY_IMAGE
The external ID for the file type representing
scanned microarray image.
|
static String |
REF_SEQ_GTF
The external ID for the file type representing a GTF
reference file that define the features on an array design
that we are interested in.
|
static String |
SAM
The external ID for the file type representing
a SAM (Sequence Alignment/Map) file.
|
static Item |
TYPE
The type of item represented by this class.
|
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
Constructor and Description |
---|
DataFileType(DataFileTypeData data)
Creates a new filetype item from the given data.
|
Modifier and Type | Method and Description |
---|---|
static DataFileType |
getByExternalId(DbControl dc,
String externalId)
Get a
DataFileType item when you know the external ID. |
static DataFileType |
getById(DbControl dc,
int id)
Get a
DataFileType object when you know the ID. |
String |
getDescription()
Get the description for the item.
|
String |
getExtension()
Get the common file extension for data files of this type.
|
String |
getExternalId()
Get the external id for the data file type.
|
ItemSubtype |
getGenericType()
Get the generic file type for this data file type.
|
ItemQuery<ItemSubtype> |
getItemSubtypes()
Get a query returning the item subtypes that files of this type
can be used on.
|
Item |
getItemType()
Get the type of item files of this type can be used on.
|
String |
getName()
Get the name of the item.
|
static DataFileType |
getNew(DbControl dc,
String externalId,
Item itemType)
Create a new data file type.
|
ItemQuery<PlatformFileType> |
getPlatforms()
Get a query that returns all platforms/variants that are using this
file type.
|
static ItemQuery<DataFileType> |
getQuery()
Get a query configured to retrieve
DataFileType items. |
static ItemQuery<DataFileType> |
getQuery(FileStoreEnabled item)
Get a query configured to retrieve
DataFileType :s
that can be used on a given item. |
static ItemQuery<DataFileType> |
getQuery(Platform platform,
PlatformVariant variant,
Item itemType,
ItemSubtype genericType)
Get a query to retrieve
DataFileType :s that can be used
on specific platform/variant for a given item and/or generic file type. |
Item |
getType()
Get the type of item represented by the object.
|
Set<ItemProxy> |
getUsingItems()
Get all:
FileSetMember :s using this file type
PlatformFileType :s using this file type
|
boolean |
hasActiveValidator(DbControl dc)
Check if there is at least one extension that claims to support
validation of files of this type.
|
boolean |
isRemoved()
Check if the removed flag is set for this item.
|
boolean |
isUsed()
Check if:
A file has been tagged with this type in a file set
A platform is using this file type
|
void |
setDescription(String description)
Set the description for the item.
|
void |
setExtension(String extension)
Set the most common gile extension for data file of this
type.
|
private void |
setExternalId(String externalId) |
void |
setGenericType(ItemSubtype genericType)
Set the generic file type of this item.
|
private void |
setItemType(Item itemType) |
void |
setName(String name)
Set the name of the item.
|
void |
setRemoved(boolean removed)
Set the removed flag for this item.
|
DataFileTypeInfo |
toTransferable(DataFileTypeInfo info)
Deprecated.
In 3.3, no replacement
|
addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, initPermissions, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getId, getVersion
checkPermission, getPermissions, hasPermission
public static final Item TYPE
Item.DATAFILETYPE
,
getType()
public static final String AFFYMETRIX_CDF
public static final String AFFYMETRIX_CEL
public static final String GENERIC_RAW_DATA
public static final String GENERIC_REPORTER_MAP
public static final String GENERIC_PRINT_MAP
public static final String GENERIC_SPOT_DATA
public static final String GENERIC_EXTRAVALUE_DATA
public static final String BASEFILE_SERIAL
public static final String BASEFILE_MATRIX
public static final String BFS_METADATA
public static final String MEV_TDMS
public static final String SAM
public static final String BAM
public static final String MICROARRAY_IMAGE
public static final String REF_SEQ_GTF
public static final String FPKM_TRACKING
public static final int MAX_EXTENSION_LENGTH
setExtension(String)
,
Constant Field Valuespublic static final int MAX_EXTERNAL_ID_LENGTH
setExternalId(String)
,
Constant Field ValuesDataFileType(DataFileTypeData data)
data
- the data.public static DataFileType getNew(DbControl dc, String externalId, Item itemType)
dc
- The DbControl to use for database accessexternalId
- The external ID of the new type, must be
unique for all file typesitemType
- The type of item that files of this type can
be attached to. The item must implement the FileStoreEnabled
interfacepublic static DataFileType getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
DataFileType
object when you know the ID.dc
- The DbControl
which will be used for
permission checking and database access.id
- The ID of the item to loadDataFileType
itemItemNotFoundException
- If an item with the specified ID is not foundPermissionDeniedException
- If the logged in user doesn't have
Permission.READ
permission to the itemsBaseException
- If there is another errorpublic static DataFileType getByExternalId(DbControl dc, String externalId) throws ItemNotFoundException, PermissionDeniedException, BaseException
DataFileType
item when you know the external ID.dc
- The DbControl
which will be used for
permission checking and database access.externalId
- The external ID of the item to loadDataFileType
item.ItemNotFoundException
- If an item with the specified ID is not foundPermissionDeniedException
- If the logged in user doesn't have
read permission for the itemBaseException
- If there is another errorpublic static ItemQuery<DataFileType> getQuery() throws BaseException
DataFileType
items.ItemQuery
objectBaseException
- If getting the query fails.public static ItemQuery<DataFileType> getQuery(FileStoreEnabled item)
DataFileType
:s
that can be used on a given item. This method will check the
FileStoreEnabled.getPlatform()
and FileStoreEnabled.getVariant()
values and restrict the query to only return items that can be used for
that platform. If the item isn't attached to any platform or variant
all data file types for the Identifiable.getType()
are returned.item
- The item to get data file types for, or null
to return all data file typesItemQuery
objectpublic static ItemQuery<DataFileType> getQuery(Platform platform, PlatformVariant variant, Item itemType, ItemSubtype genericType)
DataFileType
:s that can be used
on specific platform/variant for a given item and/or generic file type.
All parameters are optional. If all are null the result is the same
as getQuery()
.platform
- The platform, or null to not restrict by platform (unless
a variant is given)variant
- The platform variant, or null to not restrict by variantitemType
- The type of item it should be possible to
attach file to, or null to not restrict by itemgenericType
- The generic file type, or null to not restrict
by file typepublic Item getType()
Identifiable
Item
enumeration.getType
in interface Identifiable
public String getName()
Nameable
public void setName(String name) throws PermissionDeniedException, InvalidDataException
Nameable
Nameable.MAX_NAME_LENGTH
constant.setName
in interface Nameable
name
- The new name for the itemPermissionDeniedException
- If the logged in user doesn't
have write permissionInvalidDataException
- If the name is null or longer
than specified by the Nameable.MAX_NAME_LENGTH
constantpublic String getDescription()
Nameable
getDescription
in interface Nameable
String
with a description of the itempublic void setDescription(String description) throws PermissionDeniedException, InvalidDataException
Nameable
Nameable.MAX_DESCRIPTION_LENGTH
constant.setDescription
in interface Nameable
description
- The new description for the itemPermissionDeniedException
- If the logged in user doesn't
have write permissionInvalidDataException
- If the description longer
than specified by the Nameable.MAX_DESCRIPTION_LENGTH
constantpublic boolean isRemoved()
Removable
public void setRemoved(boolean removed) throws PermissionDeniedException
Removable
setRemoved
in interface Removable
removed
- TRUE if the item should be flagged as removed,
FALSE otherwisePermissionDeniedException
- If the logged in user doesn't
have Permission.DELETE
permission for setting the flag
to TRUE or Permission.WRITE
permission for setting the
flag to FALSEpublic boolean isUsed() throws BaseException
isUsed
in class BasicItem<DataFileTypeData>
BaseException
- If not able to tell if item is used or not.BasicItem.getUsingItems()
public Set<ItemProxy> getUsingItems()
FileSetMember
:s using this file type
PlatformFileType
:s using this file type
getUsingItems
in class BasicItem<DataFileTypeData>
BasicItem.addUsingItems(Set, Item, org.hibernate.Query)
@Deprecated public DataFileTypeInfo toTransferable(DataFileTypeInfo info)
ToTransferable
toTransferable
in interface ToTransferable<DataFileTypeInfo>
info
- The transferable object to usepublic String getExternalId()
private void setExternalId(String externalId) throws PermissionDeniedException, InvalidDataException, BaseException
public ItemSubtype getGenericType()
public void setGenericType(ItemSubtype genericType)
genericType
- The generic file typePermissionDeniedException
- If the logged in user doesn't
have write permissionpublic String getExtension()
public void setExtension(String extension)
extension
- The extension or nullPermissionDeniedException
- If the logged in user doesn't
have write permissionStringTooLongException
- If the string is longer that MAX_EXTENSION_LENGTH
.private void setItemType(Item itemType)
public Item getItemType()
FileStoreEnabled
interface.Item
objectpublic ItemQuery<ItemSubtype> getItemSubtypes()
getItemType()
is a Subtypable
item.public boolean hasActiveValidator(DbControl dc)
public ItemQuery<PlatformFileType> getPlatforms()