Package net.sf.basedb.core

Class Protocol

java.lang.Object
net.sf.basedb.core.BasicItem
net.sf.basedb.core.OwnedItem
net.sf.basedb.core.SharedItem
net.sf.basedb.core.CommonItem
net.sf.basedb.core.AnnotatedItem
net.sf.basedb.core.Protocol
All Implemented Interfaces:
AccessControlled, Annotatable, FileAttachable, Identifiable, Nameable, Ownable, Registered, Removable, Shareable, Subtypable
public class Protocol
extends AnnotatedItem
implements FileAttachable, Registered, Subtypable
This class is used to represent individual protocol items and information about them.
Version:
2.0
Author:
enell

  • Field Details

    • TYPE

      public static final Item TYPE
      The type of item represented by this class.
      See Also:
      Item.PROTOCOL, getType()

    • SAMPLING

      public static final String SAMPLING
      The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.
      Since:
      3.0
      See Also:
      Constant Field Values

    • EXTRACTION

      public static final String EXTRACTION
      The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.
      Since:
      3.0
      See Also:
      Constant Field Values

    • LABELING

      public static final String LABELING
      The ID for the labeling protocol type, for example a protocol used when creating a labeled extract from an Extract.
      Since:
      3.0
      See Also:
      Constant Field Values

    • LIBRARY_PREPARATION

      public static final String LIBRARY_PREPARATION
      The ID for the library preparation protocol type, for example a protocol used when creating a library extract from an Extract.
      Since:
      3.0
      See Also:
      Constant Field Values

    • POOLING

      public static final String POOLING
      The ID for the pooling protocol type, for example a protocol used when creating a biomaterial item (Sample or Extract) from a set of other biomaterial items.
      Since:
      3.0
      See Also:
      Constant Field Values

    • HYBRIDIZATION

      public static final String HYBRIDIZATION
      The ID for the hybridization protocol type, for example a protocol used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.
      Since:
      3.0
      See Also:
      Constant Field Values

    • CLUSTER_GENERATION

      public static final String CLUSTER_GENERATION
      The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.
      Since:
      3.0
      See Also:
      Constant Field Values

    • SEQUENCING

      public static final String SEQUENCING
      The ID for the sequencing protocol type, for example a protocol used when creating a DerivedBioAssay from a PhysicalBioAssay
      Since:
      3.0
      See Also:
      Constant Field Values

    • ALIGNMENT

      public static final String ALIGNMENT
      The ID for the alignment protocol type, for example a protocol used when creating a DerivedBioAssay representing data that has been aligned against a reference genome.
      Since:
      3.0
      See Also:
      Constant Field Values

    • PRINTING

      public static final String PRINTING
      The ID for the printing protocol type, for example a protocol used when printing a batch of array slides using a print robot.
      Since:
      3.0
      See Also:
      Constant Field Values

    • SCANNING

      public static final String SCANNING
      The ID for the scanning protocol type, for example a protocol used for scanning the microarray slide after an experiment.
      Since:
      3.0
      See Also:
      Constant Field Values

    • FEATURE_EXTRACTION

      public static final String FEATURE_EXTRACTION
      The ID for the feature extraction protocol type, for example a protocol used for analysing one or more images to create a raw data file.
      Since:
      3.0
      See Also:
      Constant Field Values

    • MAX_EXTERNAL_ID_LENGTH

      public static final int MAX_EXTERNAL_ID_LENGTH
      The maximum length of the external id that can be stored in the database.
      Since:
      2.15
      See Also:
      setExternalId(String), Constant Field Values

  • Constructor Details

    • Protocol

      Protocol​(ProtocolData data)
      Creates a new protocol item.
      Parameters:
      data - the data

  • Method Details