gov.usda.gdpc
Class AbstractGenotypeGroup

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

All Implemented Interfaces:

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

Direct Known Subclasses:

DefaultGenotypeGroup

public abstract class AbstractGenotypeGroup

extends AbstractDBElementGroup

implements GenotypeGroup

This class provides a skeletal implementation of the GenotypeGroup 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

AbstractGenotypeGroup()
AbstractGenotypeGroup constructor.

AbstractGenotypeGroup(Genotype[] genotypes)
AbstractGenotypeGroup constructor.

AbstractGenotypeGroup(GenotypeGroup[] groups)
AbstractGenotypeGroup constructor.

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

Method Summary

Genotype	getGenotype(java.lang.String dataSource, Taxon taxon, GenotypeExperiment experiment) Gets the genotype having the given taxon, genotype experiment, number, and data source.
GenotypeExperimentGroup	getGenotypeExperimentGroup() Returns the group of genotype experiments associated with this group of genotypes.
GenotypeGroup	getGenotypeGroup(GenotypeFilter filter) Get the genotype group from this group which match the critera specified by the filter.
TaxonGroup	getTaxonGroup() Returns the group of taxon associated with this group of genotypes.
java.lang.String	getType() Get type of this group.
int	numGenotypeExperiments() Return the number of genotype 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

AbstractGenotypeGroup

public AbstractGenotypeGroup(Genotype[] genotypes)

AbstractGenotypeGroup constructor.

Parameters:

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

AbstractGenotypeGroup

public AbstractGenotypeGroup()

AbstractGenotypeGroup constructor. Creates an empty group.

AbstractGenotypeGroup

public AbstractGenotypeGroup(java.util.List list)

AbstractGenotypeGroup constructor.

Parameters:

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

AbstractGenotypeGroup

public AbstractGenotypeGroup(GenotypeGroup[] groups)

AbstractGenotypeGroup 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 genotypes.

Specified by:

getTaxonGroup in interface GenotypeGroup

Returns:

taxon group

getGenotypeExperimentGroup

public GenotypeExperimentGroup getGenotypeExperimentGroup()

Returns the group of genotype experiments associated with this group of genotypes.

Specified by:

getGenotypeExperimentGroup in interface GenotypeGroup

Returns:

genotype experiment group

getGenotype

public Genotype getGenotype(java.lang.String dataSource,
                            Taxon taxon,
                            GenotypeExperiment experiment)

Gets the genotype having the given taxon, genotype experiment, number, and data source.

Specified by:

getGenotype in interface GenotypeGroup

Parameters:

dataSource - data source

taxon - taxon

experiment - genotype experiment

Returns:

genotype. null if no matching genotype

getGenotypeGroup

public GenotypeGroup getGenotypeGroup(GenotypeFilter filter)

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

Specified by:

getGenotypeGroup in interface GenotypeGroup

Parameters:

filter - genotype filter

Returns:

genotype group

numGenotypeExperiments

public int numGenotypeExperiments()

Return the number of genotype experiments.

Specified by:

numGenotypeExperiments in interface GenotypeGroup

Returns:

number of genotype experiments.

numTaxa

public int numTaxa()

Return the number of taxa.

Specified by:

numTaxa in interface GenotypeGroup

Returns:

number of taxa.

getType

public java.lang.String getType()

Get type of this group.

Specified by:

getType in interface DBElementGroup

Returns:

type