gov.usda.gdpc
Class Phenotype

java.lang.Object
  gov.usda.gdpc.AbstractDBElement
      gov.usda.gdpc.Phenotype

All Implemented Interfaces:

java.lang.Comparable, DBElement, java.util.Map

public class Phenotype

extends AbstractDBElement

This is a database element representing a phenotype.

Author:

terryc

Nested Class Summary

Nested classes inherited from class java.util.Map

java.util.Map.Entry

Field Summary

static java.lang.String

TYPE

Fields inherited from class gov.usda.gdpc.AbstractDBElement

myProperties

Method Summary

static java.lang.String	buildKey(java.util.Map properties) This builds the unique key for this phenotype based on the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.ONTOLOGY.
static java.lang.String	buildKey(java.lang.String dataSource, Taxon taxon, EnvironmentExperiment experiment, PhenotypeOntology ontology) This builds the unique key for this phenotype based on the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.ONTOLOGY.
static Phenotype	getCachedInstance(java.util.Map properties) This returns the phenotype instance given specified id and source.
java.lang.String	getDataSource() Returns the data source of this phenotype.
EnvironmentExperiment	getEnvironmentExperiment() Returns the environment experiment associated with this phenotype.
static Phenotype	getInstance(java.util.Map properties) This returns the phenotype instance given the specified list of properties.
java.lang.String	getName() Returns the name of this phenotype.
PhenotypeOntology	getOntology() Returns the ontology of this phenotype.
Taxon	getTaxon() Returns the taxon associated with this phenotype.
java.lang.String	getType() Get type of this element.
java.lang.String	getValue() Returns the value of this phenotype.

Methods inherited from class gov.usda.gdpc.AbstractDBElement

clear, compareTo, containsKey, containsValue, entrySet, equals, get, getID, getKey, getProperty, isEmpty, keySet, numProperties, properties, propsEqual, put, putAll, remove, size, toString, values

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

hashCode

Field Detail

TYPE

public static final java.lang.String TYPE

See Also:

Constant Field Values

Method Detail

getInstance

public static Phenotype getInstance(java.util.Map properties)

This returns the phenotype instance given the specified list of properties. A new phenotype will be created if its not found in the cache.

Parameters:

properties - properties of this phenotype. The keys are the properties (type: PhenotypeProperty) and the values are the corresponding value. Properties can not have a value equal to null. It is not allowed to have two keys that are the same. The PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.ONTOLOGY, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.VALUE properties must be defined.

Returns:

phenotype

getCachedInstance

public static Phenotype getCachedInstance(java.util.Map properties)

This returns the phenotype instance given specified id and source. Null will be returned if its not found in the cache.

Parameters:

properties - properties of this phenotype. The keys are the properties (type: PhenotypeProperty) and the values are the corresponding value. Properties can not have a value equal to null. Only the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.ONTOLOGY, PhenotypeProperty.TAXON, and PhenotypeProperty.ENVIRONMENT_EXPERIMENT are used to find a matching phenotype in the cache.

Returns:

cached phenotype or null if not in cache.

getName

public java.lang.String getName()

Returns the name of this phenotype.

Specified by:

getName in interface DBElement

Overrides:

getName in class AbstractDBElement

Returns:

the name

buildKey

public static java.lang.String buildKey(java.util.Map properties)

This builds the unique key for this phenotype based on the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.ONTOLOGY.

Parameters:

properties - properties map

Returns:

key

buildKey

public static java.lang.String buildKey(java.lang.String dataSource,
                                        Taxon taxon,
                                        EnvironmentExperiment experiment,
                                        PhenotypeOntology ontology)

This builds the unique key for this phenotype based on the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.ONTOLOGY.

Parameters:

dataSource - data source

taxon - taxon

experiment - environment experiment

ontology - phenotype ontology

Returns:

key

getDataSource

public java.lang.String getDataSource()

Returns the data source of this phenotype.

Specified by:

getDataSource in interface DBElement

Overrides:

getDataSource in class AbstractDBElement

Returns:

data source

getTaxon

public Taxon getTaxon()

Returns the taxon associated with this phenotype.

Returns:

taxon

getEnvironmentExperiment

public EnvironmentExperiment getEnvironmentExperiment()

Returns the environment experiment associated with this phenotype.

Returns:

environment experiment

getOntology

public PhenotypeOntology getOntology()

Returns the ontology of this phenotype.

Returns:

ontology

getValue

public java.lang.String getValue()

Returns the value of this phenotype.

Returns:

value

getType

public java.lang.String getType()

Get type of this element.

Returns:

type