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java.lang.Object net.sf.basedb.core.RawDataType
public class RawDataType
This class holds information about a raw data type. Unlike many other
classes this information is not stored in the database, but in the
raw-data-types.xml
XML file. This file is parsed upon
startup by the RawDataTypes
class.
Raw data types are important for RawBioAssay
:s.
RawDataTypes
,
RawBioAssay
Field Summary | |
---|---|
private int |
channels
|
private String |
description
|
private boolean |
fileOnly
|
private List<IntensityFormula> |
formulas
|
private String |
id
|
private boolean |
isAffymetrix
|
private String |
name
|
private Map<String,IntensityFormula> |
namedFormulas
|
private Map<String,RawDataProperty> |
namedProperties
|
private PlatformData |
platform
|
private List<RawDataProperty> |
properties
|
private RealTable |
realTable
|
private String |
table
|
private PlatformVariantData |
variant
|
Constructor Summary | |
---|---|
(package private) |
RawDataType(PlatformData platform)
Create a new raw data type representing a file-only platform. |
(package private) |
RawDataType(PlatformVariantData variant)
Create a new raw data type representing a file-only platform variant. |
private |
RawDataType(String id,
String name,
String description,
int channels,
boolean fileOnly,
PlatformData platform,
PlatformVariantData variant,
boolean isAffymetrix,
String table,
List<RawDataProperty> properties,
List<IntensityFormula> formulas)
|
(package private) |
RawDataType(String id,
String name,
String description,
int channels,
String table,
List<RawDataProperty> properties,
List<IntensityFormula> formulas)
Create a new RawDataType . |
Method Summary | |
---|---|
int |
compareTo(RawDataType o)
Compare the id:s of the raw data types. |
boolean |
equals(Object obj)
|
int |
getChannels()
The number of channels in this raw data type. |
String |
getDescription()
Get a description of this raw data type. |
String |
getEntityName()
|
String |
getId()
Get the id of this raw data type. |
IntensityFormula |
getIntensityFormula(String name)
|
List<IntensityFormula> |
getIntensityFormulas()
|
String |
getName()
Get the name of this raw data type. |
Platform |
getPlatform(DbControl dc)
Get the platform that this raw data type is associated with. |
(package private) PlatformData |
getPlatformProxy()
Needed to make RawBioAssay.setRawDataType(RawDataType)
backwards compatible. |
List<RawDataProperty> |
getProperties()
Get a list of RawDataProperty :s with definitions for the
extra properties that has been defined for this raw data type. |
RawDataProperty |
getProperty(String name)
|
RawData |
getRawDataById(DbControl dc,
int id)
|
RealTable |
getRealTable()
|
String |
getTableName()
Get the name of the database table that is used to store the extra properties of this raw data type. |
PlatformVariant |
getVariant(DbControl dc)
Get the platform variant that this raw data type is associated with. |
(package private) PlatformVariantData |
getVariantProxy()
Needed to make RawBioAssay.setRawDataType(RawDataType)
backwards compatible. |
int |
hashCode()
|
boolean |
isAffymetrix()
Deprecated. Use getPlatform(DbControl) and compare
the external ID with Platform.AFFYMETRIX |
boolean |
isStoredInDb()
If the raw data of this raw data type can be stored in the database or not. |
(package private) void |
setName(String name)
Update the name. |
String |
toString()
|
Methods inherited from class java.lang.Object |
---|
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
private final String id
private String name
private final String description
private final boolean fileOnly
private final boolean isAffymetrix
private final int channels
private final PlatformData platform
private final PlatformVariantData variant
private String table
private RealTable realTable
private List<RawDataProperty> properties
private Map<String,RawDataProperty> namedProperties
private List<IntensityFormula> formulas
private Map<String,IntensityFormula> namedFormulas
Constructor Detail |
---|
RawDataType(String id, String name, String description, int channels, String table, List<RawDataProperty> properties, List<IntensityFormula> formulas)
RawDataType
.
See the getter methods for a description of the parameters
RawDataType(PlatformData platform)
platform
- The platformRawDataType(PlatformVariantData variant)
variant
- The platform variantprivate RawDataType(String id, String name, String description, int channels, boolean fileOnly, PlatformData platform, PlatformVariantData variant, boolean isAffymetrix, String table, List<RawDataProperty> properties, List<IntensityFormula> formulas)
Method Detail |
---|
public String getId()
id
attribute of the <raw-data-type>
tag in the XML file.
public boolean isAffymetrix()
getPlatform(DbControl)
and compare
the external ID with Platform.AFFYMETRIX
public Platform getPlatform(DbControl dc)
isStoredInDb()
returns true this
method will always return null.
dc
- The DbControl to use for database access
public PlatformVariant getVariant(DbControl dc)
dc
- The DbControl to use for database access
PlatformData getPlatformProxy()
RawBioAssay.setRawDataType(RawDataType)
backwards compatible. Platforms that are not file-only will
get the Platform.GENERIC
platform.
PlatformVariantData getVariantProxy()
RawBioAssay.setRawDataType(RawDataType)
backwards compatible.
public String getName()
name
attribute of the <raw-data-type>
tag in the XML file. The name is not used by the core, but should be used
by client applications in the user interface.
void setName(String name)
public String getDescription()
description
attribute of the <raw-data-type>
tag in the XML file. The description is not used by the core, but can be used
by client applications in help texts, etc.
public int getChannels()
channels
attribute of the <raw-data-type>
tag in the XML file.
public boolean isStoredInDb()
getTableName()
public String getTableName()
table
attribute of the <raw-data-type>
tag in the XML file. The table name is normally not useful for
any client application.
isStoredInDb()
public String getEntityName()
public RealTable getRealTable()
public List<RawDataProperty> getProperties()
RawDataProperty
:s with definitions for the
extra properties that has been defined for this raw data type.
List
object containing RawDataProperty
objectspublic RawDataProperty getProperty(String name)
public List<IntensityFormula> getIntensityFormulas()
public IntensityFormula getIntensityFormula(String name)
public String toString()
toString
in class Object
public RawData getRawDataById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
ItemNotFoundException
PermissionDeniedException
BaseException
public int compareTo(RawDataType o)
compareTo
in interface Comparable<RawDataType>
public boolean equals(Object obj)
equals
in class Object
public int hashCode()
hashCode
in class Object
|
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