gov.nih.nci.caarray.domain.array
Class Gene

java.lang.Object
  extended by gov.nih.nci.caarray.domain.AbstractCaArrayObject
      extended by gov.nih.nci.caarray.domain.AbstractCaArrayEntity
          extended by gov.nih.nci.caarray.domain.array.Gene
All Implemented Interfaces:
com.fiveamsolutions.nci.commons.data.persistent.PersistentObject, java.io.Serializable

public class Gene
extends AbstractCaArrayEntity

A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism. The functional and physical unit of heredity passed from parent to offspring.

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Serialized Form

Field Summary
static java.lang.String ENSEMBLE
          Name of the Ensemble database.
static java.lang.String ENTREZ_GENE
          Name of the Entrez Gene database.
static java.lang.String GENBANK
          Name of the GenBank database.
static java.lang.String REF_SEQ
          Name of the RefSeq database.
static java.lang.String THC
          Name of the THC database.
static java.lang.String UNIGENE
          Name of the UniGene database.
 
Fields inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
CAARRAY_LSID_AUTHORITY, CAARRAY_LSID_NAMESPACE
 
Fields inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayObject
DEFAULT_BATCH_SIZE, DEFAULT_STRING_COLUMN_SIZE, LARGE_TEXT_FIELD_LENGTH
 
Constructor Summary
Gene()
           
 
Method Summary
 void addAccessionNumber(java.lang.String databaseName, java.lang.String accessionNumber)
          Add an accession to this gene.
 java.util.List<java.lang.String> getAccessionNumbers(java.lang.String databaseName)
          Get all the accessions associated with this gene in the given public database.
 java.lang.String getEnsemblgeneID()
           
 java.lang.String getEntrezgeneID()
           
 java.lang.String getFullName()
           
 java.lang.String getGenbankAccession()
           
 java.lang.String getGenbankAccessionVersion()
           
 java.lang.String getRefseqAccession()
           
 java.lang.String getSymbol()
           
 java.lang.String getThcAccession()
           
 java.lang.String getUnigeneclusterID()
           
 void setEnsemblgeneID(java.lang.String ensemblgeneID)
           
 void setEntrezgeneID(java.lang.String entrezgeneID)
           
 void setFullName(java.lang.String fullName)
           
 void setGenbankAccession(java.lang.String genbankAccession)
           
 void setGenbankAccessionVersion(java.lang.String genbankAccessionVersion)
           
 void setRefseqAccession(java.lang.String refseqAccession)
           
 void setSymbol(java.lang.String symbol)
           
 void setThcAccession(java.lang.String thcAccession)
           
 void setUnigeneclusterID(java.lang.String unigeneclusterID)
           
 
Methods inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
getLsid, getLsidAuthority, getLsidNamespace, getLsidObjectId, setLsid, setLsid, setLsidForEntity
 
Methods inherited from class gov.nih.nci.caarray.domain.AbstractCaArrayObject
equals, getCaBigId, getId, getPostLoadSecurityPolicies, getRemoteApiSecurityPolicies, hashCode, setCaBigId, setId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

UNIGENE

public static final java.lang.String UNIGENE
Name of the UniGene database.

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Constant Field Values

GENBANK

public static final java.lang.String GENBANK
Name of the GenBank database.

See Also:
Constant Field Values

ENTREZ_GENE

public static final java.lang.String ENTREZ_GENE
Name of the Entrez Gene database.

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Constant Field Values

ENSEMBLE

public static final java.lang.String ENSEMBLE
Name of the Ensemble database.

See Also:
Constant Field Values

REF_SEQ

public static final java.lang.String REF_SEQ
Name of the RefSeq database.

See Also:
Constant Field Values

THC

public static final java.lang.String THC
Name of the THC database.

See Also:
Constant Field Values
Constructor Detail

Gene

public Gene()
Method Detail

getSymbol

public java.lang.String getSymbol()
Returns:
the symbol

setSymbol

public void setSymbol(java.lang.String symbol)
Parameters:
symbol - the symbol to set

getFullName

@Length(max=2000)
public java.lang.String getFullName()
Returns:
the fullName

setFullName

public void setFullName(java.lang.String fullName)
Parameters:
fullName - the fullName to set

getEnsemblgeneID

public java.lang.String getEnsemblgeneID()
Returns:
the ensemblgeneID

setEnsemblgeneID

public void setEnsemblgeneID(java.lang.String ensemblgeneID)
Parameters:
ensemblgeneID - the ensemblgeneID to set

getEntrezgeneID

public java.lang.String getEntrezgeneID()
Returns:
the entrezgeneID

setEntrezgeneID

public void setEntrezgeneID(java.lang.String entrezgeneID)
Parameters:
entrezgeneID - the entrezgeneID to set

getGenbankAccession

public java.lang.String getGenbankAccession()
Returns:
the genbankAccession

setGenbankAccession

public void setGenbankAccession(java.lang.String genbankAccession)
Parameters:
genbankAccession - the genbankAccession to set

getGenbankAccessionVersion

public java.lang.String getGenbankAccessionVersion()
Returns:
the genbankAccessionVersion

setGenbankAccessionVersion

public void setGenbankAccessionVersion(java.lang.String genbankAccessionVersion)
Parameters:
genbankAccessionVersion - the genbankAccessionVersion to set

getUnigeneclusterID

public java.lang.String getUnigeneclusterID()
Returns:
the unigeneclusterID

setUnigeneclusterID

public void setUnigeneclusterID(java.lang.String unigeneclusterID)
Parameters:
unigeneclusterID - the unigeneclusterID to set

getRefseqAccession

public java.lang.String getRefseqAccession()
Returns:
the refseqAccession

setRefseqAccession

public void setRefseqAccession(java.lang.String refseqAccession)
Parameters:
refseqAccession - the refseqAccession to set

getThcAccession

public java.lang.String getThcAccession()
Returns:
the thcAccession

setThcAccession

public void setThcAccession(java.lang.String thcAccession)
Parameters:
thcAccession - the thcAccession to set

addAccessionNumber

public void addAccessionNumber(java.lang.String databaseName,
                               java.lang.String accessionNumber)
Add an accession to this gene.

Parameters:
databaseName - the name of the public database.
accessionNumber - the accession number to add.

getAccessionNumbers

public java.util.List<java.lang.String> getAccessionNumbers(java.lang.String databaseName)
Get all the accessions associated with this gene in the given public database.

Parameters:
databaseName - the name of the public database.
Returns:
a list of accessions.