org.forester.ws.seqdb

Class UniProtEntry

java.lang.Object

org.forester.ws.seqdb.UniProtEntry

All Implemented Interfaces:

SequenceDatabaseEntry

public final class UniProtEntry
extends Object
implements SequenceDatabaseEntry

Field Summary

Fields

Modifier and Type	Field and Description
static Pattern	BindingDB_PATTERN
static Pattern	CTD_PATTERN
static Pattern	DrugBank_PATTERN
static Pattern	GO_PATTERN
static Pattern	HGNC_PATTERN
static Pattern	KEGG_PATTERN
static Pattern	MIM_PATTERN
static Pattern	NCBI_TAXID_PATTERN
static Pattern	NextBio_PATTERN
static Pattern	Orphanet_PATTERN
static Pattern	PDB_PATTERN
static Pattern	PharmGKB_PATTERN
static Pattern	Reactome_PATTERN

Method Summary

Modifier and Type	Method and Description
Object	clone()
static SequenceDatabaseEntry	createInstanceFromPlainText(List<String> lines)
String	getAccession()
SortedSet<Annotation>	getAnnotations()
String	getChromosome()
SortedSet<Accession>	getCrossReferences()
String	getGeneName()
SortedSet<GoTerm>	getGoTerms()
String	getMap()
MolecularSequence	getMolecularSequence()
String	getProvider()
String	getSequenceName()
String	getSequenceSymbol()
String	getTaxonomyIdentifier()
String	getTaxonomyScientificName()
boolean	isEmpty()

Methods inherited from class java.lang.Object

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

Field Detail

BindingDB_PATTERN

public static final Pattern BindingDB_PATTERN

CTD_PATTERN

public static final Pattern CTD_PATTERN

DrugBank_PATTERN

public static final Pattern DrugBank_PATTERN

GO_PATTERN

public static final Pattern GO_PATTERN

KEGG_PATTERN

public static final Pattern KEGG_PATTERN

MIM_PATTERN

public static final Pattern MIM_PATTERN

NextBio_PATTERN

public static final Pattern NextBio_PATTERN

Orphanet_PATTERN

public static final Pattern Orphanet_PATTERN

PDB_PATTERN

public static final Pattern PDB_PATTERN

PharmGKB_PATTERN

public static final Pattern PharmGKB_PATTERN

Reactome_PATTERN

public static final Pattern Reactome_PATTERN

HGNC_PATTERN

public static final Pattern HGNC_PATTERN

NCBI_TAXID_PATTERN

public static final Pattern NCBI_TAXID_PATTERN

Method Detail

clone

public Object clone()
             throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

getAccession

public String getAccession()

Specified by:

getAccession in interface SequenceDatabaseEntry

getCrossReferences

public SortedSet<Accession> getCrossReferences()

Specified by:

getCrossReferences in interface SequenceDatabaseEntry

getGeneName

public String getGeneName()

Specified by:

getGeneName in interface SequenceDatabaseEntry

getGoTerms

public SortedSet<GoTerm> getGoTerms()

Specified by:

getGoTerms in interface SequenceDatabaseEntry

getProvider

public String getProvider()

Specified by:

getProvider in interface SequenceDatabaseEntry

getSequenceName

public String getSequenceName()

Specified by:

getSequenceName in interface SequenceDatabaseEntry

getSequenceSymbol

public String getSequenceSymbol()

Specified by:

getSequenceSymbol in interface SequenceDatabaseEntry

getTaxonomyIdentifier

public String getTaxonomyIdentifier()

Specified by:

getTaxonomyIdentifier in interface SequenceDatabaseEntry

getTaxonomyScientificName

public String getTaxonomyScientificName()

Specified by:

getTaxonomyScientificName in interface SequenceDatabaseEntry

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface SequenceDatabaseEntry

createInstanceFromPlainText

public static SequenceDatabaseEntry createInstanceFromPlainText(List<String> lines)

getAnnotations

public SortedSet<Annotation> getAnnotations()

Specified by:

getAnnotations in interface SequenceDatabaseEntry

getMap

public String getMap()

Specified by:

getMap in interface SequenceDatabaseEntry

getChromosome

public String getChromosome()

Specified by:

getChromosome in interface SequenceDatabaseEntry

getMolecularSequence

public MolecularSequence getMolecularSequence()

Specified by:

getMolecularSequence in interface SequenceDatabaseEntry