com.hfg.bio.taxonomy.ncbi

Class NCBITaxon

java.lang.Object

com.hfg.bio.taxonomy.ncbi.NCBITaxon

All Implemented Interfaces:

Comparable<NCBITaxon>

public class NCBITaxon
extends Object
implements Comparable<NCBITaxon>

Species class based on the NCBI taxonomy data. A default set of files are included as data sources. To minimize load time and memory the initial default data source has a few common values. If a value is requested that isn't found in this set, a second, more complete but not fully up-to-date data source is loaded and the lightweight data source is discarded. An additional more up-to-date data source can be manually added as an NCBIRemoteTaxonomyDataSource.

Field Summary

Fields

Modifier and Type	Field and Description
static NCBITaxon	BOS_TAURUS Cow
static NCBITaxon	CAMELUS_BACTRIANUS Camel
static NCBITaxon	CAMELUS_DROMEDARIUS Dromedary
static NCBITaxon	CANIS_FAMILIARIS Dog
static NCBITaxon	CRICETULUS_GRISEUS Hamster
static NCBITaxon	DROSOPHILA_MELANOGASTER Drosophila (Fruit fly)
static NCBITaxon	EQUUS_CABALLUS Horse
static NCBITaxon	ESCHERICHIA_COLI E.
static NCBITaxon	HOMO_SAPIENS Human
static NCBITaxon	LAMA_GLAMA Llama
static NCBITaxon	MACACA_MULATTA Rhesus monkey
static NCBITaxon	MAMMALS Mammals
static NCBITaxon	MUS_MUSCULUS Mouse
static NCBITaxon	ORYCTOLAGUS_CUNICULUS Rabbit
static NCBITaxon	OVIS_ARIES Sheep
static NCBITaxon	PAN_TROGLODYTES Chimpanzee
static NCBITaxon	PRIMATES Primates
static NCBITaxon	RATTUS_NORVEGICUS Rat
static NCBITaxon	RODENTS Rodents
static NCBITaxon	SACCHAROMYCES_CEREVISIAE Yeast
static NCBITaxon	SUS_SCROFA Pig
static NCBITaxon	SYNTHETIC_CONSTRUCT Synthetic construct / artificial sequence
static NCBITaxon	UNKNOWN Unknown / unidentified
static NCBITaxon	VICUGNA_PACOS Alpaca
static NCBITaxon	XENOPUS_LAEVIS Xenopus (African clawed frog)

Constructor Summary

Constructors

Constructor and Description
NCBITaxon(int inTaxonId)

Method Summary

Modifier and Type	Method and Description
static void	addDataSource(int inIndex, NCBITaxonomyDataSource inValue)
static void	addDataSource(NCBITaxonomyDataSource inValue)
NCBITaxon	addSynonym(String inValue)
int	compareTo(NCBITaxon inObj)
boolean	equals(Object inObj)
static void	exportNamesFile(Set<Integer> inTaxonIds, File inDestFile) Creates a subset of the names file containing just the specified taxon ids (and their parent taxon ids).
static void	exportNodesFile(Set<Integer> inTaxonIds, File inDestFile) Creates a subset of the nodes file containing just the specified taxon ids (and their parent taxon ids).
static Set<NCBITaxon>	getByName(String inValue) Retrieves the NCBITaxon for the specified common name, scientific name, or GenBank common name.
static NCBITaxon	getByTaxonId(int inValue) Returns the taxon for the specified NCBI taxon id.
String	getComments()
String	getCommonName()
static Collection<NCBITaxon>	getCommonSet() Returns an unmodifiable Collection of the common taxons (those defined as class constants).
NCBIGenBankDivision	getDivision()
String	getEMBL_Code()
NCBITaxon	getFirstCommonTaxon(NCBITaxon inTaxon2)
String	getFullTaxonomy()
String	getGenBankCommonName()
boolean	getGenBankHiddenFlag()
NCBIGeneticCode	getGeneticCode()
boolean	getHiddenSubtreeRootFlag()
boolean	getInheritedDivisionFlag()
boolean	getInheritedGeneticCodeFlag()
boolean	getInheritedMitochondrialGeneticCodeFlag()
static Logger	getLogger()
NCBIGeneticCode	getMitochondrialGeneticCode()
NCBITaxon	getParentTaxon()
int	getParentTaxonId()
String	getScientificName()
Set<String>	getSynonyms()
int	getTaxonId()
NCBITaxonNodeRank	getTaxonomyRank()
int	hashCode()
boolean	isSubtaxonOf(NCBITaxon inTaxon2)
NCBITaxon	setComments(String inValue)
NCBITaxon	setCommonName(String inValue)
static void	setDataSource(NCBITaxonomyDataSource inValue)
NCBITaxon	setDivision(NCBIGenBankDivision inValue)
NCBITaxon	setEMBL_Code(String inValue)
NCBITaxon	setGenBankCommonName(String inValue)
NCBITaxon	setGenBankHiddenFlag(boolean inValue)
NCBITaxon	setGeneticCode(NCBIGeneticCode inValue)
NCBITaxon	setHiddenSubtreeRootFlag(boolean inValue)
NCBITaxon	setInheritedDivisionFlag(boolean inValue)
NCBITaxon	setInheritedGeneticCodeFlag(boolean inValue)
NCBITaxon	setInheritedMitochondrialGeneticCodeFlag(boolean inValue)
NCBITaxon	setMitochondrialGeneticCode(NCBIGeneticCode inValue)
NCBITaxon	setParentTaxonId(int inValue)
NCBITaxon	setScientificName(String inValue)
NCBITaxon	setSynonyms(Collection<String> inValues)
NCBITaxon	setTaxonomyRank(NCBITaxonNodeRank inValue)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

HOMO_SAPIENS

public static final NCBITaxon HOMO_SAPIENS

Human

MUS_MUSCULUS

public static final NCBITaxon MUS_MUSCULUS

Mouse

RATTUS_NORVEGICUS

public static final NCBITaxon RATTUS_NORVEGICUS

Rat

CRICETULUS_GRISEUS

public static final NCBITaxon CRICETULUS_GRISEUS

Hamster

ORYCTOLAGUS_CUNICULUS

public static final NCBITaxon ORYCTOLAGUS_CUNICULUS

Rabbit

BOS_TAURUS

public static final NCBITaxon BOS_TAURUS

Cow

EQUUS_CABALLUS

public static final NCBITaxon EQUUS_CABALLUS

Horse

SUS_SCROFA

public static final NCBITaxon SUS_SCROFA

Pig

OVIS_ARIES

public static final NCBITaxon OVIS_ARIES

Sheep

XENOPUS_LAEVIS

public static final NCBITaxon XENOPUS_LAEVIS

Xenopus (African clawed frog)

DROSOPHILA_MELANOGASTER

public static final NCBITaxon DROSOPHILA_MELANOGASTER

Drosophila (Fruit fly)

ESCHERICHIA_COLI

public static final NCBITaxon ESCHERICHIA_COLI

E. Coli

SACCHAROMYCES_CEREVISIAE

public static final NCBITaxon SACCHAROMYCES_CEREVISIAE

Yeast

CANIS_FAMILIARIS

public static final NCBITaxon CANIS_FAMILIARIS

Dog

PAN_TROGLODYTES

public static final NCBITaxon PAN_TROGLODYTES

Chimpanzee

MACACA_MULATTA

public static final NCBITaxon MACACA_MULATTA

Rhesus monkey

CAMELUS_BACTRIANUS

public static final NCBITaxon CAMELUS_BACTRIANUS

Camel

CAMELUS_DROMEDARIUS

public static final NCBITaxon CAMELUS_DROMEDARIUS

Dromedary

LAMA_GLAMA

public static final NCBITaxon LAMA_GLAMA

Llama

VICUGNA_PACOS

public static final NCBITaxon VICUGNA_PACOS

Alpaca

MAMMALS

public static final NCBITaxon MAMMALS

Mammals

PRIMATES

public static final NCBITaxon PRIMATES

Primates

RODENTS

public static final NCBITaxon RODENTS

Rodents

UNKNOWN

public static final NCBITaxon UNKNOWN

Unknown / unidentified

SYNTHETIC_CONSTRUCT

public static final NCBITaxon SYNTHETIC_CONSTRUCT

Synthetic construct / artificial sequence

Constructor Detail

NCBITaxon

public NCBITaxon(int inTaxonId)

Method Detail

getLogger

public static Logger getLogger()

addDataSource

public static void addDataSource(NCBITaxonomyDataSource inValue)

addDataSource

public static void addDataSource(int inIndex,
                                 NCBITaxonomyDataSource inValue)

setDataSource

public static void setDataSource(NCBITaxonomyDataSource inValue)

getByName

public static Set<NCBITaxon> getByName(String inValue)

Retrieves the NCBITaxon for the specified common name, scientific name, or GenBank common name. Generally there will be a single taxon found for a given name, but there are instances where multiple taxons may be found.

Parameters:

inValue - the species name (common or scientific) for the taxon object to return

Returns:

a Set of taxon objects corresponding to the specified name. Returns null if a match cannot be found.

getByTaxonId

public static NCBITaxon getByTaxonId(int inValue)

Returns the taxon for the specified NCBI taxon id.

Parameters:

inValue - the taxon id for the taxon object to retrieve

Returns:

the taxon object corresponding to the specified id

getCommonSet

public static Collection<NCBITaxon> getCommonSet()

Returns an unmodifiable Collection of the common taxons (those defined as class constants).

Returns:

the small collection of frequently used taxon objects

toString

public String toString()

Overrides:

toString in class Object

getTaxonId

public int getTaxonId()

getFullTaxonomy

public String getFullTaxonomy()

isSubtaxonOf

public boolean isSubtaxonOf(NCBITaxon inTaxon2)

getFirstCommonTaxon

public NCBITaxon getFirstCommonTaxon(NCBITaxon inTaxon2)

getParentTaxon

public NCBITaxon getParentTaxon()

setParentTaxonId

public NCBITaxon setParentTaxonId(int inValue)

getParentTaxonId

public int getParentTaxonId()

getScientificName

public String getScientificName()

setScientificName

public NCBITaxon setScientificName(String inValue)

getCommonName

public String getCommonName()

setCommonName

public NCBITaxon setCommonName(String inValue)

getGenBankCommonName

public String getGenBankCommonName()

setGenBankCommonName

public NCBITaxon setGenBankCommonName(String inValue)

getSynonyms

public Set<String> getSynonyms()

setSynonyms

public NCBITaxon setSynonyms(Collection<String> inValues)

addSynonym

public NCBITaxon addSynonym(String inValue)

getTaxonomyRank

public NCBITaxonNodeRank getTaxonomyRank()

setTaxonomyRank

public NCBITaxon setTaxonomyRank(NCBITaxonNodeRank inValue)

getEMBL_Code

public String getEMBL_Code()

setEMBL_Code

public NCBITaxon setEMBL_Code(String inValue)

getDivision

public NCBIGenBankDivision getDivision()

setDivision

public NCBITaxon setDivision(NCBIGenBankDivision inValue)

getInheritedDivisionFlag

public boolean getInheritedDivisionFlag()

setInheritedDivisionFlag

public NCBITaxon setInheritedDivisionFlag(boolean inValue)

getGeneticCode

public NCBIGeneticCode getGeneticCode()

setGeneticCode

public NCBITaxon setGeneticCode(NCBIGeneticCode inValue)

getInheritedGeneticCodeFlag

public boolean getInheritedGeneticCodeFlag()

setInheritedGeneticCodeFlag

public NCBITaxon setInheritedGeneticCodeFlag(boolean inValue)

getMitochondrialGeneticCode

public NCBIGeneticCode getMitochondrialGeneticCode()

setMitochondrialGeneticCode

public NCBITaxon setMitochondrialGeneticCode(NCBIGeneticCode inValue)

getInheritedMitochondrialGeneticCodeFlag

public boolean getInheritedMitochondrialGeneticCodeFlag()

setInheritedMitochondrialGeneticCodeFlag

public NCBITaxon setInheritedMitochondrialGeneticCodeFlag(boolean inValue)

getGenBankHiddenFlag

public boolean getGenBankHiddenFlag()

setGenBankHiddenFlag

public NCBITaxon setGenBankHiddenFlag(boolean inValue)

getHiddenSubtreeRootFlag

public boolean getHiddenSubtreeRootFlag()

setHiddenSubtreeRootFlag

public NCBITaxon setHiddenSubtreeRootFlag(boolean inValue)

getComments

public String getComments()

setComments

public NCBITaxon setComments(String inValue)

equals

public boolean equals(Object inObj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

compareTo

public int compareTo(NCBITaxon inObj)

Specified by:

compareTo in interface Comparable<NCBITaxon>

exportNodesFile

public static void exportNodesFile(Set<Integer> inTaxonIds,
                                   File inDestFile)

Creates a subset of the nodes file containing just the specified taxon ids (and their parent taxon ids).

Parameters:

inTaxonIds - the list of id to extract from the taxonomy data

inDestFile - the nodes file to which the extracted taxon data should be written

exportNamesFile

public static void exportNamesFile(Set<Integer> inTaxonIds,
                                   File inDestFile)
                            throws IOException

Creates a subset of the names file containing just the specified taxon ids (and their parent taxon ids).

Parameters:

inTaxonIds - the list of id to extract from the taxonomy data

inDestFile - the names file to which the extracted taxon data should be written

Throws:

IOException