gov.usda.gdpc
Class AbstractPhenotypeGroup

java.lang.Object
  gov.usda.gdpc.AbstractGroup
      gov.usda.gdpc.AbstractDBElementGroup
          gov.usda.gdpc.AbstractPhenotypeGroup

All Implemented Interfaces:

java.util.Collection, DBElementGroup, Group, java.util.List, PhenotypeGroup

Direct Known Subclasses:

DefaultPhenotypeGroup

public abstract class AbstractPhenotypeGroup

extends AbstractDBElementGroup

implements PhenotypeGroup

This class provides a skeletal implementation of the PhenotypeGroup interface to minimize the effort required to implement this interface.

Author:

terryc

Field Summary

Fields inherited from class gov.usda.gdpc.AbstractDBElementGroup

myIndex

Constructor Summary

AbstractPhenotypeGroup()
AbstractPhenotypeGroup constructor.

AbstractPhenotypeGroup(java.util.List list)
AbstractPhenotypeGroup constructor.

AbstractPhenotypeGroup(Phenotype[] phenotypes)
AbstractPhenotypeGroup constructor.

AbstractPhenotypeGroup(PhenotypeGroup[] groups)
AbstractPhenotypeGroup constructor.

Method Summary

EnvironmentExperimentGroup	getEnvironmentExperimentGroup() Returns the group of environment experiments associated with this group of phenotypes.
Phenotype	getPhenotype(java.lang.String dataSource, Taxon taxon, EnvironmentExperiment experiment, PhenotypeOntology ontology) Gets the phenotype having the given taxon, environment experiment, ontology, and data source.
PhenotypeGroup	getPhenotypeGroup(PhenotypeFilter filter) Get the phenotype group from this group which match the critera specified by the filter.
TaxonGroup	getTaxonGroup() Returns the group of taxon associated with this group of phenotypes.
java.lang.String	getType() Get type of this group.
int	numEnvironmentExperiments() Return the number of phenotype experiments.
int	numTaxa() Return the number of taxa.

Methods inherited from class gov.usda.gdpc.AbstractDBElementGroup

getDBElementGroup, getDBElements, getDefinedProperties, getDistinctProperties, index, toString

Methods inherited from class gov.usda.gdpc.AbstractGroup

add, add, addAll, addAll, clear, contains, containsAll, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from class java.lang.Object

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

Methods inherited from interface gov.usda.gdpc.DBElementGroup

getDBElements, getDefinedProperties, getDistinctProperties, index

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Constructor Detail

AbstractPhenotypeGroup

public AbstractPhenotypeGroup(Phenotype[] phenotypes)

AbstractPhenotypeGroup constructor.

Parameters:

phenotypes - list of phenotypes to be a part of this group.

AbstractPhenotypeGroup

public AbstractPhenotypeGroup()

AbstractPhenotypeGroup constructor. Creates an empty group.

AbstractPhenotypeGroup

public AbstractPhenotypeGroup(java.util.List list)

AbstractPhenotypeGroup constructor.

Parameters:

list - list of objects to be a part of this group. Any null in the list will be discarded.

AbstractPhenotypeGroup

public AbstractPhenotypeGroup(PhenotypeGroup[] groups)

AbstractPhenotypeGroup constructor.

Parameters:

groups - groups to include in this new group.

Method Detail

getTaxonGroup

public TaxonGroup getTaxonGroup()

Returns the group of taxon associated with this group of phenotypes.

Specified by:

getTaxonGroup in interface PhenotypeGroup

Returns:

taxon group

getEnvironmentExperimentGroup

public EnvironmentExperimentGroup getEnvironmentExperimentGroup()

Returns the group of environment experiments associated with this group of phenotypes.

Specified by:

getEnvironmentExperimentGroup in interface PhenotypeGroup

Returns:

environment experiment group

getPhenotype

public Phenotype getPhenotype(java.lang.String dataSource,
                              Taxon taxon,
                              EnvironmentExperiment experiment,
                              PhenotypeOntology ontology)

Gets the phenotype having the given taxon, environment experiment, ontology, and data source.

Specified by:

getPhenotype in interface PhenotypeGroup

Parameters:

dataSource - data source

taxon - taxon

experiment - environment experiment

ontology - phenotype ontology

Returns:

phenotype. null if no matching phenotype

getPhenotypeGroup

public PhenotypeGroup getPhenotypeGroup(PhenotypeFilter filter)

Get the phenotype group from this group which match the critera specified by the filter.

Specified by:

getPhenotypeGroup in interface PhenotypeGroup

Parameters:

filter - phenotype filter

Returns:

phenotype group

numEnvironmentExperiments

public int numEnvironmentExperiments()

Return the number of phenotype experiments.

Specified by:

numEnvironmentExperiments in interface PhenotypeGroup

Returns:

number of environment experiments.

numTaxa

public int numTaxa()

Return the number of taxa.

Specified by:

numTaxa in interface PhenotypeGroup

Returns:

number of taxa.

getType

public java.lang.String getType()

Get type of this group.

Specified by:

getType in interface DBElementGroup

Returns:

type