gov.nih.nci.caarray.domain.project
Enum ExperimentOntologyCategory

java.lang.Object
  extended by java.lang.Enum<ExperimentOntologyCategory>
      extended by gov.nih.nci.caarray.domain.project.ExperimentOntologyCategory
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<ExperimentOntologyCategory>

public enum ExperimentOntologyCategory
extends java.lang.Enum<ExperimentOntologyCategory>

Enum of Ontology categories for various concepts used in caarray The majority of these categories come from the MGED ontology.


Enum Constant Summary
CELL_TYPE
          CellType category, used for cell types.
CLINICAL_DIAGNOSIS
          Clinical Diagnosis category, one of annotation fields allowed by TCGA policy.
DISEASE_STATE
          DiseaseState category, used for diseases/conditions of an experiment.
EXPERIMENT_DESIGN_TYPE
          ExperimentDesignType category, for selecting type of experiment design.
EXPERIMENTAL_FACTOR_CATEGORY
          ExperimentalFactorCategory category, for experimental factor types.
EXTERNAL_ID
          External Id, used for biomaterials.
EXTERNAL_SAMPLE_ID
          External Sample Id, used for samples.
HISTOLOGIC_DIAGNOSIS
          Histologic Diagnosis category, one of annotation fields allowed by TCGA policy.
LABEL_COMPOUND
          LabelCompound category, used for the label of a LabeledExtract.
MATERIAL_TYPE
          MaterialType category, used for tissue types.
ORGANISM
          Organism category, used for organisms.
ORGANISM_PART
          OrganismPart category, used for tissue site.
PATHOLOGIC_STATUS
          Pathologic Status category, one of annotation fields allowed by TCGA policy.
PROTOCOL_TYPE
          ProtocolType category, used for protocol types.
PUBLICATION_STATUS
          PublicationStatus category, used for status of Publications.
PUBLICATION_TYPE
          PublicationType category, used for type of Publications.
QUALITY_CONTROL_TYPE
          QualityControlDescriptionType category, for selecting type of quality control measures.
REPLICATE_TYPE
          QualityControlDescriptionType category, for selecting type of quality control measures.
ROLES
          Roles category, used for various roles in an experiment.
TECHNOLOGY_TYPE
          TechnologyType category, used for array designs.
TISSUE_ANATOMIC_SITE
          Tissue Anatomic Site category, one of annotation fields allowed by TCGA policy.
 
Method Summary
 java.lang.String getCategoryName()
           
 ExperimentOntology getOntology()
           
static ExperimentOntologyCategory valueOf(java.lang.String name)
          Returns the enum constant of this type with the specified name.
static ExperimentOntologyCategory[] values()
          Returns an array containing the constants of this enum type, in the order they are declared.
 
Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
 
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
 

Enum Constant Detail

ORGANISM

public static final ExperimentOntologyCategory ORGANISM
Organism category, used for organisms.


ORGANISM_PART

public static final ExperimentOntologyCategory ORGANISM_PART
OrganismPart category, used for tissue site.


MATERIAL_TYPE

public static final ExperimentOntologyCategory MATERIAL_TYPE
MaterialType category, used for tissue types.


CELL_TYPE

public static final ExperimentOntologyCategory CELL_TYPE
CellType category, used for cell types.


DISEASE_STATE

public static final ExperimentOntologyCategory DISEASE_STATE
DiseaseState category, used for diseases/conditions of an experiment.


LABEL_COMPOUND

public static final ExperimentOntologyCategory LABEL_COMPOUND
LabelCompound category, used for the label of a LabeledExtract.


EXPERIMENT_DESIGN_TYPE

public static final ExperimentOntologyCategory EXPERIMENT_DESIGN_TYPE
ExperimentDesignType category, for selecting type of experiment design.


QUALITY_CONTROL_TYPE

public static final ExperimentOntologyCategory QUALITY_CONTROL_TYPE
QualityControlDescriptionType category, for selecting type of quality control measures.


REPLICATE_TYPE

public static final ExperimentOntologyCategory REPLICATE_TYPE
QualityControlDescriptionType category, for selecting type of quality control measures.


ROLES

public static final ExperimentOntologyCategory ROLES
Roles category, used for various roles in an experiment.


PUBLICATION_TYPE

public static final ExperimentOntologyCategory PUBLICATION_TYPE
PublicationType category, used for type of Publications.


PUBLICATION_STATUS

public static final ExperimentOntologyCategory PUBLICATION_STATUS
PublicationStatus category, used for status of Publications.


CLINICAL_DIAGNOSIS

public static final ExperimentOntologyCategory CLINICAL_DIAGNOSIS
Clinical Diagnosis category, one of annotation fields allowed by TCGA policy.


HISTOLOGIC_DIAGNOSIS

public static final ExperimentOntologyCategory HISTOLOGIC_DIAGNOSIS
Histologic Diagnosis category, one of annotation fields allowed by TCGA policy.


PATHOLOGIC_STATUS

public static final ExperimentOntologyCategory PATHOLOGIC_STATUS
Pathologic Status category, one of annotation fields allowed by TCGA policy.


TISSUE_ANATOMIC_SITE

public static final ExperimentOntologyCategory TISSUE_ANATOMIC_SITE
Tissue Anatomic Site category, one of annotation fields allowed by TCGA policy.


TECHNOLOGY_TYPE

public static final ExperimentOntologyCategory TECHNOLOGY_TYPE
TechnologyType category, used for array designs.


EXPERIMENTAL_FACTOR_CATEGORY

public static final ExperimentOntologyCategory EXPERIMENTAL_FACTOR_CATEGORY
ExperimentalFactorCategory category, for experimental factor types.


PROTOCOL_TYPE

public static final ExperimentOntologyCategory PROTOCOL_TYPE
ProtocolType category, used for protocol types.


EXTERNAL_ID

public static final ExperimentOntologyCategory EXTERNAL_ID
External Id, used for biomaterials.


EXTERNAL_SAMPLE_ID

public static final ExperimentOntologyCategory EXTERNAL_SAMPLE_ID
External Sample Id, used for samples. This is to support legacy data sets, new data sets should use ExternalId.

Method Detail

values

public static ExperimentOntologyCategory[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
for (ExperimentOntologyCategory c : ExperimentOntologyCategory.values())
    System.out.println(c);

Returns:
an array containing the constants of this enum type, in the order they are declared

valueOf

public static ExperimentOntologyCategory valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:
name - the name of the enum constant to be returned.
Returns:
the enum constant with the specified name
Throws:
java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
java.lang.NullPointerException - if the argument is null

getCategoryName

public java.lang.String getCategoryName()
Returns:
the categoryName

getOntology

public ExperimentOntology getOntology()
Returns:
the ontology to which this category belongs