Package net.sf.basedb.core

Class RawDataType

java.lang.Object
net.sf.basedb.core.RawDataType
All Implemented Interfaces:
Comparable<RawDataType>
public class RawDataType
extends Object
implements Comparable<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.

Version:
2.0
Author:
Nicklas
See Also:
RawDataTypes, RawBioAssay
Last modified
$Date: 2014-06-04 14:41:12 +0200 (on, 04 jun 2014) $

  • Field Details

  • Constructor Details

  • Method Details

    • getId

      public String getId()
      Get the id of this raw data type. This value is the same as the id attribute of the <raw-data-type> tag in the XML file.
      Returns:
      The id for this raw data type

    • getPlatform

      public Platform getPlatform​(DbControl dc)
      Get the platform that this raw data type is associated with. Only raw data types representing file-only platforms are associated with that platform. If isStoredInDb() returns true this method will always return null.
      Parameters:
      dc - The DbControl to use for database access
      Returns:
      A Platform item or null if this raw data type isn't associated with a platform
      Since:
      2.5

    • getVariant

      public PlatformVariant getVariant​(DbControl dc)
      Get the platform variant that this raw data type is associated with. Only raw data types representing file-only variants are associated with that variant.
      Parameters:
      dc - The DbControl to use for database access
      Returns:
      A Platform item or null if this raw data type isn't associated with a variant
      Since:
      2.5

    • getName

      public String getName()
      Get the name of this raw data type. This value is the same as the 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.
      Returns:
      The name for this raw data type

    • setName

      void setName​(String name)
      Update the name. Used mainly for file-only representations of raw data types when the underlying platform is changed.
      Since:
      2.16.2

    • getDescription

      public String getDescription()
      Get a description of this raw data type. This value is the same as the 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.
      Returns:
      A description for this raw data type

    • getChannels

      public int getChannels()
      The number of channels in this raw data type. Channels are important in the core when it comes to the analysis phase. Some analysis methods only works for a specific number of channels (mostly two). This value is the same as the channels attribute of the <raw-data-type> tag in the XML file.
      Returns:
      The number of channels

    • isStoredInDb

      public boolean isStoredInDb()
      If the raw data of this raw data type can be stored in the database or not.
      See Also:
      getTableName()

    • getTableName

      public String getTableName()
      Get the name of the database table that is used to store the extra properties of this raw data type. This value is the same as the table attribute of the <raw-data-type> tag in the XML file. The table name is normally not useful for any client application.
      Returns:
      The name of the database table for this raw data type, or null if not stored in database
      See Also:
      isStoredInDb()

    • getEntityName

      public String getEntityName()

    • getRealTable

      public RealTable getRealTable()

    • getProperties

      public List<RawDataProperty> getProperties()
      Get a list of RawDataProperty:s with definitions for the extra properties that has been defined for this raw data type.
      Returns:
      A List object containing RawDataProperty objects

    • getProperty

      public RawDataProperty getProperty​(String name)

    • getIntensityFormulas

      public List<IntensityFormula> getIntensityFormulas()

    • getIntensityFormula

      public IntensityFormula getIntensityFormula​(String name)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getRawDataById

      public RawData getRawDataById​(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
      Throws:
      ItemNotFoundException
      PermissionDeniedException
      BaseException

    • compareTo

      public int compareTo​(RawDataType o)
      Compare the id:s of the raw data types. Note! Before 2.16.2 the name was used for comparing but this led to issues when changing the name of file-only plaforms. See ticket #1567.
      Specified by:
      compareTo in interface Comparable<RawDataType>
      Since:
      2.5

    • equals

      public boolean equals​(Object obj)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object