gov.usda.gdpc
Class Genotype

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

All Implemented Interfaces:

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

public class Genotype

extends AbstractDBElement

This is a database element representing a genotype.

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 GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, and GenotypeProperty.GENOTYPE_EXPERIMENT.
static java.lang.String	buildKey(java.lang.String dataSource, Taxon taxon, GenotypeExperiment experiment) This builds the unique key for this phenotype based on the GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, and GenotypeProperty.GENOTYPE_EXPERIMENT.
AlleleList	getAlleleList() Returns the allele list of this genotype.
static Genotype	getCachedInstance(java.util.Map properties) This returns the genotype instance given specified id and source.
java.lang.String	getDataSource() Returns the data source of this genotype.
GenotypeExperiment	getGenotypeExperiment() Returns the genotype experiment associated with this genotype.
static Genotype	getInstance(java.util.Map properties) This returns the genotype instance given the specified list of properties.
java.lang.String	getName() Returns the name of this genotype.
Taxon	getTaxon() Returns the taxon associated with this genotype.
java.lang.String	getType() Get type of this element.

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 Genotype getInstance(java.util.Map properties)

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

Parameters:

properties - properties of this genotype. The keys are the properties (type: GenotypeProperty) 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 GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, GenotypeProperty.GENOTYPE_EXPERIMENT, and GenotypeProperty.VALUE properties must be defined.

Returns:

genotype

getCachedInstance

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

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

Parameters:

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

Returns:

cached genotype or null if not in cache.

getName

public java.lang.String getName()

Returns the name of this genotype.

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 GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, and GenotypeProperty.GENOTYPE_EXPERIMENT.

Parameters:

properties - properties map

Returns:

key

buildKey

public static java.lang.String buildKey(java.lang.String dataSource,
                                        Taxon taxon,
                                        GenotypeExperiment experiment)

This builds the unique key for this phenotype based on the GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, and GenotypeProperty.GENOTYPE_EXPERIMENT.

Parameters:

dataSource - data source

taxon - taxon

experiment - genotype experiment

Returns:

key

getDataSource

public java.lang.String getDataSource()

Returns the data source of this genotype.

Specified by:

getDataSource in interface DBElement

Overrides:

getDataSource in class AbstractDBElement

Returns:

data source

getTaxon

public Taxon getTaxon()

Returns the taxon associated with this genotype.

Returns:

taxon

getGenotypeExperiment

public GenotypeExperiment getGenotypeExperiment()

Returns the genotype experiment associated with this genotype.

Returns:

genotype experiment

getAlleleList

public AlleleList getAlleleList()

Returns the allele list of this genotype.

Returns:

allele list

getType

public java.lang.String getType()

Get type of this element.

Returns:

type